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SMC1A Gene

protein-coding   GIFtS: 70
GCID: GC0XM053401

Structural Maintenance Of Chromosomes 1A

(Previous names: SMC1 (structural maintenance of chromosomes 1, yeast)-like...)
(Previous symbol: SMC1L1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Structural Maintenance Of Chromosomes 1A1 2     SMC1 Structural Maintenance Of Chromosomes 1-Like 1 (Yeast)1
SMC1L11 2 3     SMC1alpha2
DXS423E2 3 5     SMCB2
SMC12 3 5     Segregation Of Mitotic Chromosomes 12
SMC1 (Structural Maintenance Of Chromosomes 1, Yeast)-Like 11 2     Structural Maintenance Of Chromosomes Protein 1A2
SB1.82 3     KIAA01783
SMC-1-alpha2 3     SMC-1A3
SMC Protein 1A2 3     Sb1.83
CDLS22 5     

External Ids:    HGNC: 111111   Entrez Gene: 82432   Ensembl: ENSG000000725017   OMIM: 3000405   UniProtKB: Q146833   

Export aliases for SMC1A gene to outside databases

Previous GC identifers: GC0XM053417 GC0XM050459


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SMC1A Gene:
Proper cohesion of sister chromatids is a prerequisite for the correct segregation of chromosomes during cell
division. The cohesin multiprotein complex is required for sister chromatid cohesion. This complex is composed
partly of two structural maintenance of chromosomes (SMC) proteins, SMC3 and either SMC1B or the protein encoded
by this gene. Most of the cohesin complexes dissociate from the chromosomes before mitosis, although those
complexes at the kinetochore remain. Therefore, the encoded protein is thought to be an important part of
functional kinetochores. In addition, this protein interacts with BRCA1 and is phosphorylated by ATM, indicating
a potential role for this protein in DNA repair. This gene, which belongs to the SMC gene family, is located in
an area of the X-chromosome that escapes X inactivation. Mutations in this gene result in Cornelia de Lange
syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. (provided by
RefSeq, Jul 2013)

GeneCards Summary for SMC1A Gene:
SMC1A (structural maintenance of chromosomes 1A) is a protein-coding gene. Diseases associated with SMC1A include cornelia de lange syndrome 2, and smc1a-related cornelia de lange syndrome. GO annotations related to this gene include microtubule motor activity and protein heterodimerization activity. An important paralog of this gene is SMC1B.

UniProtKB/Swiss-Prot: SMC1A_HUMAN, Q14683
Function: Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin
complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. The cohesin
complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase,
the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin
complex may also play a role in spindle pole assembly during mitosis. Involved in DNA repair via its interaction
with BRCA1 and its related phosphorylation by ATM, or via its phosphorylation by ATR. Works as a downstream
effector both in the ATM/NBS1 branch and in the ATR/MSH2 branch of S-phase checkpoint

Gene Wiki entry for SMC1A Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000023.11  NC_018934.2  NT_011630.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMC1A gene promoter:
         NF-1   NF-1/L   p53   Pax-6   FOXO3   E4BP4   FOXO3b   HOXA5   FOXO3a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SMC1A promoter sequence
   Search Chromatin IP Primers for SMC1A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMC1A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xp11.22-p11.21   Ensembl cytogenetic band:  Xp11.22   HGNC cytogenetic band: Xp11.22-p11.21

SMC1A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMC1A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM053401:  view genomic region     (about GC identifiers)

Start:
53,401,070 bp from pter      End:
53,449,677 bp from pter
Size:
48,608 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SMC1A_HUMAN, Q14683 (See protein sequence)
Recommended Name: Structural maintenance of chromosomes protein 1A  
Size: 1233 amino acids; 143233 Da
Subunit: Interacts with POLE. Interacts with SYCP2. Interacts with BRCA1. Found in a complex with CDCA5, SMC3 and
RAD21, PDS5A/APRIN and PDS5B/SCC-112 (By similarity). Forms a heterodimer with SMC3 in cohesin complexes. Cohesin
complexes are composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domain, RAD21
which link them, and one STAG protein (STAG1, STAG2 or STAG3), which interacts with RAD21. In germ cell cohesin
complexes, SMC1A is mutually exclusive with SMC1B. Interacts with BRCA1. Interacts with NDC80. Interacts with
RPGR (By similarity)
Miscellaneous: Mutated Cornelia de Lange cell lines display genomic instability and sensitivity to ionizing
radiation and interstrand cross-linking agents
Secondary accessions: O14995 Q16351 Q2M228

Explore the universe of human proteins at neXtProt for SMC1A: NX_Q14683

Explore proteomics data for SMC1A at MOPED

Post-translational modifications: 

  • Phosphorylated by ATM upon ionizing radiation in a NBS1-dependent manner. Phosphorylated by ATR upon DNA
    methylation in a MSH2/MSH6-dependent manner. Phosphorylation of Ser-957 and Ser-966 activates it and is required
    for S-phase checkpoint activation1
  • Ubiquitination2 at Lys5, Lys13, Lys52, Lys106, Lys110, Lys170, Lys177, Lys500, Lys508, Lys536,
                                 Lys540, Lys561, Lys607, Lys637, Lys648, Lys660, Lys736, Lys1037, Lys1120, Lys1222
  • Modification sites at PhosphoSitePlus

  • See SMC1A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001268392.1  NP_006297.2  

    ENSEMBL proteins: 
     ENSP00000323421   ENSP00000476416   ENSP00000476958   ENSP00000413509   ENSP00000364489  
    Reactome Protein details: Q14683

    SMC1A Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for SMC1A
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    Novus Biologicals SMC1A Protein
    Novus Biologicals SMC1A Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SMC1A

    SMC1A Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of SMC1A
    R&D Systems Antibodies for SMC1A (SMC1)
    Cell Signaling Technology (CST) Antibodies for SMC1A  (Smc1)
    OriGene Antibodies for SMC1A
    OriGene Custom Antibody Services for SMC1A
    Novus Biologicals SMC1A Antibodies
    Abcam antibodies for SMC1A
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    ThermoFisher Antibody for SMC1A
    LSBio Antibodies in human, mouse, rat for SMC1A

    SMC1A Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for SMC1A
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SMC1A
    Cloud-Clone Corp. CLIAs for SMC1A


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SMC: Structural maintenance of chromosomes proteins

    5 InterPro protein domains:
     IPR003395 RecF/RecN/SMC_N
     IPR027417 P-loop_NTPase
     IPR024704 SMC
     IPR028468 Smc1
     IPR010935 SMC_hinge

    Graphical View of Domain Structure for InterPro Entry Q14683

    ProtoNet protein and cluster: Q14683

    1 Blocks protein domain: IPB010935 SMCs flexible hinge

    UniProtKB/Swiss-Prot: SMC1A_HUMAN, Q14683
    Domain: The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the
    heterotypic interaction with the corresponding domain of SMC3, forming a V-shaped heterodimer. The two heads of
    the heterodimer are then connected by different ends of the cleavable RAD21 protein, forming a ring structure (By
    similarity)
    Similarity: Belongs to the SMC family. SMC1 subfamily


    SMC1A for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SMC1A_HUMAN, Q14683
    Function: Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin
    complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. The cohesin
    complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase,
    the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin
    complex may also play a role in spindle pole assembly during mitosis. Involved in DNA repair via its interaction
    with BRCA1 and its related phosphorylation by ATM, or via its phosphorylation by ATR. Works as a downstream
    effector both in the ATM/NBS1 branch and in the ATR/MSH2 branch of S-phase checkpoint

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003682chromatin binding IDA11076961
    GO:0003777microtubule motor activity NAS12199140
    GO:0005515protein binding IPI11877377
    GO:0005524ATP binding IEA--
    GO:0036033mediator complex binding IEA--
         
    SMC1A for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SMC1A:
     Increased Salmonella enterica  

         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Smc1a):
     cellular  hematopoietic system  immune system  mortality/aging 

    SMC1A for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMC1A
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SMC1A

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SMC1A
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SMC1A

    miRNA
    Products:
        
    miRTarBase miRNAs that target SMC1A:
    hsa-let-7b-5p (MIRT052108), hsa-mir-423-3p (MIRT042579), hsa-mir-615-3p (MIRT040012), hsa-mir-21-5p (MIRT031051), hsa-mir-92a-3p (MIRT049569), hsa-mir-328-3p (MIRT043786), hsa-mir-339-5p (MIRT042788), hsa-mir-744-5p (MIRT037710), hsa-mir-93-3p (MIRT038730), hsa-mir-320a (MIRT044450), hsa-let-7e-5p (MIRT004469), hsa-mir-149-5p (MIRT045613)

    Block miRNA regulation of human, mouse, rat SMC1A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SMC1A (see all 97):
    hsa-miR-640 hsa-miR-520f hsa-miR-605 hsa-miR-371-5p hsa-miR-4275 hsa-miR-877* hsa-miR-149 hsa-miR-383
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for SMC1A
    Predesigned siRNA for gene silencing in human, mouse, rat SMC1A

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: SMC1A (NM_006306)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SMC1A
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMC1A

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMC1A


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SMC1A_HUMAN, Q14683: Nucleus. Chromosome. Chromosome, centromere, kinetochore. Note=Associates with chromatin.
    Before prophase it is scattered along chromosome arms. During prophase, most of cohesin complexes dissociate from
    chromatin probably because of phosphorylation by PLK, except at centromeres, where cohesin complexes remain. At
    anaphase, the RAD21 subunit of the cohesin complex is cleaved, leading to the dissociation of the complex from
    chromosomes, allowing chromosome separation. In germ cells, cohesin complex dissociates from chromatin at
    prophase I, and may be replaced by a meiosis-specific cohesin complex. The phosphorylated form on Ser-957 and
    Ser-966 associates with chromatin during G1/S/G2 phases but not during M phase, suggesting that phosphorylation
    does not regulate cohesin function. Integral component of the functional centromere-kinetochore complex at the
    kinetochore region during mitosis
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol4

    Gene Ontology (GO): Selected cellular component terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000775chromosome, centromeric region TAS--
    GO:0000776kinetochore IDA11682612
    GO:0000777condensed chromosome kinetochore IEA--
    GO:0000794condensed nuclear chromosome TAS7757074
    GO:0005634nucleus IDA--

    SMC1A for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SMC1A About   (see all 17)  
    See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    mRNA Splicing - Major Pathway0.78
    mRNA Splicing0.78
    Processing of Capped Intron-Containing Pre-mRNA0.78
    mRNA processing0.44
    2Cell cycle
    Cell cycle0.59
    Cell cycle0.59
    3Mitotic Metaphase and Anaphase
    Mitotic Anaphase0.94
    Mitotic Metaphase and Anaphase0.93
    Separation of Sister Chromatids0.94
    4Cell Cycle, Mitotic
    Cell Cycle, Mitotic0.90
    M Phase0.62
    Cell Cycle0.90
    5Mitotic Prometaphase
    Mitotic Prometaphase0.92
    Resolution of Sister Chromatid Cohesion0.92

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SMC1A
        ATM Pathway
    Mitotic Roles of Polo Like Kinases

    3 Cell Signaling Technology (CST) Pathways for SMC1A
        Chromatin Regulation / Acetylation
    Cell Cycle / Checkpoint Control
    DNA Damage

    2 GeneGo (Thomson Reuters) Pathways for SMC1A
        DNA damage ATM/ATR regulation of G1/S checkpoint
    Cell cycle Spindle assembly and chromosome separation

    4 BioSystems Pathways for SMC1A
        Cell cycle
    DNA damage response
    mRNA processing
    RB in Cancer

    Selected Reactome Pathways for SMC1A (see all 6)
        mRNA Splicing - Major Pathway
    Cohesin Loading onto Chromatin
    Establishment of Sister Chromatid Cohesion
    Resolution of Sister Chromatid Cohesion
    Separation of Sister Chromatids


    2 Kegg Pathways  (Kegg details for SMC1A):
        Cell cycle
    Oocyte meiosis


    SMC1A for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including SMC1A: 
              Cell Cycle in human mouse rat
              DNA Damage Signaling Pathway in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SMC1A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SMC1A (Q146831, 2, 3 ENSP000003234214) via UniProtKB, MINT, STRING, and/or I2D (see all 1095)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000070mitotic sister chromatid segregation TAS7757074
    GO:0000278mitotic cell cycle TAS--
    GO:0000398mRNA splicing, via spliceosome TAS--
    GO:0006281DNA repair TAS11877377
    GO:0006310DNA recombination IEA--

    SMC1A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SMC1A

    2 Novoseek inferred chemical compound relationships for SMC1A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    phosphatidylinositol 14.1 1 11877376 (1)
    doxorubicin 13.5 3 15489221 (2)



    SMC1A for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SMC1A gene (2 alternative transcripts): 
    NM_001281463.1  NM_006306.3  

    Unigene Cluster for SMC1A:

    Structural maintenance of chromosomes 1A
    Hs.211602  [show with all ESTs]
    Unigene Representative Sequence: NM_006306
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000322213(uc004dsg.3 uc011moe.2) ENST00000470241 ENST00000469129
    ENST00000463684 ENST00000428014 ENST00000375340(uc011mof.2)
    miRNA
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    Block miRNA regulation of human, mouse, rat SMC1A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SMC1A (see all 97):
    hsa-miR-640 hsa-miR-520f hsa-miR-605 hsa-miR-371-5p hsa-miR-4275 hsa-miR-877* hsa-miR-149 hsa-miR-383
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    GenScript: all cDNA clones in your preferred vector: SMC1A (NM_006306)
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    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SMC1A
      QuantiTect SYBR Green Assays in human, mouse, rat SMC1A
      QuantiFast Probe-based Assays in human, mouse, rat SMC1A

    Additional mRNA sequence: 

    AF176781.1 AK055575.1 AK056308.1 AK091458.1 AK291921.1 AK301266.1 BC064368.1 BC080185.1 
    BC112127.1 BC171726.1 BX640922.1 D80000.2 

    12 DOTS entries:

    DT.446814  DT.101976237  DT.95186644  DT.91683482  DT.100791702  DT.100791703  DT.121301618  DT.95222590 
    DT.97779204  DT.102823459  DT.95186643  DT.95186646 

    Selected AceView cDNA sequences (see all 390):

    AI795827 BM988187 AA369747 AI990887 CA442769 AI733693 AA314169 AW271698 
    BQ576192 AA228103 AA598887 BE881200 BI057117 BQ187642 BM679402 AW076005 
    AA836056 AA588031 BI862357 BQ422461 BQ023226 AW169949 AJ430451 AI561204 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SMC1A (see all 7)    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^
    SP1:              -     -                                                                             -                                                         
    SP2:                                                                                                                                                            
    SP3:              -     -     -     -     -                                                                                                                     
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 21 ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25a · 25b ^ 26a · 26b
    SP1:                          -           -                     
    SP2:                                                            
    SP3:                                                            
    SP4:                                                            
    SP5:                                                            


    ECgene alternative splicing isoforms for SMC1A

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SMC1A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTACTTAATG
    SMC1A Expression
    About this image


    SMC1A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 10) fully expand
     
     Brain (Nervous System)    fully expand to see all 6 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Metencephalon
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Kidney (Urinary System)
             Metanephros
    SMC1A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMC1A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.211602
        Pathway & Disease-focused RT2 Profiler PCR Arrays including SMC1A: 
              Cell Cycle in human mouse rat
              DNA Damage Signaling Pathway in human mouse rat

    Primer
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMC1A

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for SMC1A gene from Selected species (see all 27)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smc1a1 , 5 structural maintenance of chromosomes 1A1, 5 92.43(n)1
    99.84(a)1
      X (68.46 cM)5
    240611  NM_019710.21  NP_062684.21 
     1520164285 
    chicken
    (Gallus gallus)
    Aves SMC1A1 structural maintenance of chromosomes 1A 81.72(n)
    94.57(a)
      395187  NM_204516.1  NP_989847.1 
    lizard
    (Anolis carolinensis)
    Reptilia SMC1A6
    structural maintenance of chromosomes 1A
    96(a)
    1 ↔ 1
    2(89317710-89353774)
    African clawed frog
    (Xenopus laevis)
    Amphibia smc1l1-prov2 SMC-like 1 (yeast) 83.09(n)    BC046691.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.247712 Danio rerio cDNA clone IMAGE6034135, partial cds 79.13(n)    BC055212.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta SMC11 SMC1 55.82(n)
    50.17(a)
      42853  NM_142954.3  NP_651211.2 
    worm
    (Caenorhabditis elegans)
    Secernentea him-11 him-1 51.03(n)
    43.45(a)
      172116  NM_001047193.4  NP_001040658.2 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SMC1(YFL008W)4
    SMC11
    Subunit of the multiprotein cohesin complex, essential more4
    SMC11
    45.84(n)1
    33.93(a)1
      6(119429-123106)4
    8505401, 4  NP_116647.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons TTN81 TTN8 49.84(n)
    39.39(a)
      824632  NM_001203163.1  NP_001190092.1 
    rice
    (Oryza sativa)
    Liliopsida Os.83352 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 75.67(n)    AK120333.1 


    ENSEMBL Gene Tree for SMC1A (if available)
    TreeFam Gene Tree for SMC1A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SMC1A gene
    SMC1B2  
    3 SIMAP similar genes for SMC1A using alignment to 8 protein entries:     SMC1A_HUMAN (see all proteins):
    DKFZp686L19178    SMC1B    SMC4

    SMC1A for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SMC1A (see all 604)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0627914
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0627912 R Q mis40--------
    VAR_0627884
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0627882 R H mis40--------
    VAR_0627874
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0627872 E K mis40--------
    VAR_0628014
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0628012 Y C mis40--------
    VAR_0645424
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0645422 R Q mis40--------
    VAR_0645434
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0645432 I T mis40--------
    VAR_0627984
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0627982 R Q mis40--------
    VAR_0627974
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0627972 C F mis40--------
    VAR_0265294
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0265292 E A mis40--------
    VAR_0627994
    Cornelia de Lange syndrome 2 (CDLS2)4--see VAR_0627992 R G mis40--------

    HapMap Linkage Disequilibrium report for SMC1A (53401070 - 53449677 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SMC1A:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2740175CNV Deletion23290073
    nsv435891CNV Deletion17901297
    nsv6908CNV Insertion18451855

    Human Gene Mutation Database (HGMD): SMC1A
    Locus Specific Mutation Databases (LSDB): SMC1A

    Site Specific Mutation Identification with PCR Assays
    1 Copy Number PCR Panel containing SMC1A:
    Intellectual Disability
    SeqTarget long-range PCR primers for resequencing SMC1A
    DNA2.0 Custom Variant and Variant Library Synthesis for SMC1A

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300040   
    OMIM disorders: 300590  
    UniProtKB/Swiss-Prot: SMC1A_HUMAN, Q14683
  • Cornelia de Lange syndrome 2 (CDLS2) [MIM:300590]: A form of Cornelia de Lange syndrome, a clinically
    heterogeneous developmental disorder associated with malformations affecting multiple systems. Characterized by
    facial dysmorphisms, abnormal hands and feet, growth delay, cognitive retardation, hirsutism, gastroesophageal
    dysfunction and cardiac, ophthalmologic and genitourinary anomalies. Note=The disease is caused by mutations
    affecting the gene represented in this entry

  • Selected diseases for SMC1A (see all 29):    
    About MalaCards
    cornelia de lange syndrome 2    smc1a-related cornelia de lange syndrome    sc phocomelia syndrome    roberts syndrome
    cornelia de lange syndrome    cornelia de lange syndrome 1    nijmegen breakage syndrome    ataxia telangiectasia
    hypertrophic cardiomyopathy    ataxia    retinitis pigmentosa    intellectual disability
    kaposi's sarcoma    acute myeloid leukemia    retinitis    mental retardation
    sarcoma    pneumonia    myeloid leukemia    hypoxia

    3 diseases from the University of Copenhagen DISEASES database for SMC1A:
    Cornelia de Lange syndrome     SC phocomelia syndrome     Intellectual disability

    SMC1A for disorders           About GeneDecksing

    2 Novoseek inferred disease relationships for SMC1A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ataxia telangiectasia 83.8 5 19147735 (2), 15752898 (1)
    nijmegen breakage syndrome 73.4 1 15752898 (1)

    GeneTests: SMC1A
    GeneReviews: SMC1A
    Genetic Association Database (GAD): SMC1A
    Human Genome Epidemiology (HuGE) Navigator: SMC1A (1 document)

    Export disorders for SMC1A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SMC1A gene, integrated from 10 sources (see all 157):
    (articles sorted by number of sources associating them with SMC1A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The human SB1.8 gene (DXS423E) encodes a putative chromosome segregation protein conserved in lower eukaryotes and prokaryotes. (PubMed id 7757074)1, 2, 3, 9 Rocques P.J.... Cooper C.S. (Hum. Mol. Genet. 1995)
    2. Mutations and variants in the cohesion factor genes NIPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lange syndrome. (PubMed id 20358602)1, 2, 4 Pie J....Ramos F.J. (Am. J. Med. Genet. A 2010)
    3. SMC1 is a downstream effector in the ATM/NBS1 branch of the human S- phase checkpoint. (PubMed id 11877377)1, 2, 9 Yazdi P.T.... Qin J. (Genes Dev. 2002)
    4. MSH2 and ATR form a signaling module and regulate two branches of the damage response to DNA methylation. (PubMed id 14657349)1, 2, 9 Wang Y. and Qin J. (Proc. Natl. Acad. Sci. U.S.A. 2003)
    5. Hypertrophic cardiomyopathy in a girl with Cornelia de Lange syndrome due to mutation in SMC1A. (PubMed id 20635401)1, 2 Limongelli G.... Larizza L. (Am. J. Med. Genet. A 2010)
    6. Cornelia de Lange syndrome mutations in SMC1A or SMC3 affect binding to DNA. (PubMed id 18996922)1, 2 Revenkova E.... Musio A. (Hum. Mol. Genet. 2009)
    7. SMC1A expression and mechanism of pathogenicity in probands with X- Linked Cornelia de Lange syndrome. (PubMed id 19701948)1, 2 Liu J.... Krantz I.D. (Hum. Mutat. 2009)
    8. Mutations in cohesin complex members SMC3 and SMC1A cause a mild variant of Cornelia de Lange syndrome with predominant mental retardation. (PubMed id 17273969)1, 2 Deardorff M.A....Krantz I.D. (Am. J. Hum. Genet. 2007)
    9. X-linked Cornelia de Lange syndrome owing to SMC1L1 mutations. (PubMed id 16604071)1, 2 Musio A.... Larizza L. (Nat. Genet. 2006)
    10. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 8243 HGNC: 11111 AceView: SMC1L1 Ensembl:ENSG00000072501 euGenes: HUgn8243
    ECgene: SMC1A Kegg: 8243 H-InvDB: SMC1A

    (According to HUGE)
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    HUGE: KIAA0178

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for SMC1A Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SMC1A[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SMC1A gene:
    Search GeneIP for patents involving SMC1A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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