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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SMC1A Gene

protein-coding   GIFtS: 70
GCID: GC0XM053417

Structural Maintenance Of Chromosomes 1A

(Previous names: SMC1 (structural maintenance of chromosomes 1, yeast)-like...)
(Previous symbol: SMC1L1)
Microbiology & Infectious Diseases Congress
  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)
About This Section

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 identifer: GC0XM050459


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 smc1a-related cornelia de lange syndrome, and cornelia de lange syndrome, and among its related super-pathways are mRNA Processing and Cell cycle. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.2  NT_011630.14  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for SMC1A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 GC0XM053417:  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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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)
Subcellular location: 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
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:

  • UniProtKB: 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 activation
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q14683

  • SMC1A Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SMC1A Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001268392.1  NP_006297.2  

    ENSEMBL proteins: 
     ENSP00000323421   ENSP00000413509   ENSP00000364489  
    Reactome Protein details: Q14683
    Human Recombinant Protein Products 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 

    Gene Ontology (GO): 5/12 cellular component terms (GO ID links to tree view) (see all 12):    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



    SMC1A Antibody Products: 
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    Abcam antibodies for SMC1A
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    LSBio Antibodies in human, mouse, rat for SMC1A 

    Assay Products for SMC1A: 
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    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)
    About This Section
    HGNC Gene Families: 
    SMC: Structural maintenance of chromosomes proteins

    4 InterPro protein domains:
     IPR027417 P-loop_NTPase
     IPR003395 RecF/RecN/SMC
     IPR024704 SMC
     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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    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): 5/6 molecular function terms (GO ID links to tree view) (see all 6):    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 - Custom generated mouse model solutions for SMC1A 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions 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
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    miRTarBase miRNAs that target SMC1A:
    hsa-let-7e (MIRT004469)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SMC1A
    8/97 QIAGEN miScript miRNA 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
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMC1A


    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for SMC1A About   (see all 15)                                                                                              See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    Processing of Capped Intron-Containing Pre-mRNA0.85
    mRNA Splicing0.82
    mRNA Processing0.85
    mRNA processing0.46
    mRNA Splicing - Major Pathway0.82
    2Cell cycle
    Cell cycle0.59
    Cell cycle0.59
    3M Phase
    Mitotic Anaphase0.94
    M Phase0.88
    Separation of Sister Chromatids0.94
    Mitotic M-M/G1 phases0.88
    Mitotic Metaphase and Anaphase0.94
    4Cohesin Loading onto Chromatin
    Cohesin Loading onto Chromatin0.71
    Establishment of Sister Chromatid Cohesion0.62
    Mitotic Telophase/Cytokinesis0.71
    5Meiotic Synapsis
    Meiotic Synapsis0.70
    Chromosome Maintenance0.56
    Meiosis0.70

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 EMD Millipore Pathways for SMC1A
        DNA damage ATM/ATR regulation of G1/S checkpoint
    Cell cycle Spindle assembly and chromosome separation


    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

    3 BioSystems Pathways for SMC1A
        DNA damage response
    Cell cycle
    mRNA processing

    5/21        Reactome Pathways for SMC1A (see all 21)
        Establishment of Sister Chromatid Cohesion
    Mitotic Prometaphase
    Resolution of Sister Chromatid Cohesion
    mRNA Splicing
    Cell Cycle


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


    SMC1A for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SMC1A

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

    5/1042 Interacting proteins for SMC1A (Q146831, 2, 3 ENSP000003234214) via UniProtKB, MINT, STRING, and/or I2D (see all 1042)
    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): 5/21 biological process terms (GO ID links to tree view) (see all 21):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000070mitotic sister chromatid segregation TAS7757074
    GO:0000075cell cycle checkpoint ----
    GO:0000278mitotic cell cycle TAS--
    GO:0000398mRNA splicing, via spliceosome TAS--
    GO:0000910cytokinesis ----

    SMC1A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    SMC1A for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    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)

    Search CenterWatch for drugs/clinical trials and news about SMC1A

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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)
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    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 

    24/390 AceView cDNA sequences (see all 390):

    AA228103 AA836056 AI433133 AL561226 AK091458 BQ187642 BU191891 AI561204 
    BQ184545 BG120710 BP375393 AW080425 CA433892 BU859457 CA389997 BQ437793 
    BI222464 BM784470 AI702217 AA329880 BM128619 BU956395 BU688340 BX470568 

    GeneLoc Exon Structure

    5/7 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SMC1A expression in normal human tissues (normalized intensities)      SMC1A embryonic expression: see
    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 
     5/15 selected tissues (see all 15) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
             brain/midbrain   
     
     Limb (Muscoskeletal System)    fully expand to see all 2 entries
             limb/hindlimb   
     
     Nose (Sensory Organs)    fully expand to see all 2 entries
             sensory organ/nose/nasal cavity   
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Metencephalon
     
     Eye (Sensory Organs)
             Retina

    See SMC1A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SMC1A

    SOURCE GeneReport for Unigene cluster: Hs.211602
        SABiosciences Expression via Pathway-Focused 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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for SMC1A gene from 10/27 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 81.78(n)
    94.57(a)
      395187  NM_204516.1  NP_989847.1 
    lizard
    (Anolis carolinensis)
    Reptilia SMC1A6
    Uncharacterized protein
    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 CG6057-PA 55.63(n)
    49.75(a)
      42853  NM_142954.3  NP_651211.2 
    worm
    (Caenorhabditis elegans)
    Secernentea him-11 Protein HIM-1 50.67(n)
    43.08(a)
      172116  NM_001047193.3  NP_001040658.2 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SMC1(YFL008W)4
    SMC11
    Subunit of the multiprotein cohesin complex, essential more4
    Smc1p1
    44.4(n)1
    32.09(a)1
      6(119429-123106)4
    8505401, 4  NP_116647.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons TTN81 structural maintenance of chromosomes 1 49.65(n)
    38.55(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)
    About This Section
    Paralogs for SMC1A gene
    SMC1B2  
    3 SIMAP similar genes for SMC1A using alignment to 6 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/604 SNPs in SMC1A are shown (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
    SABiosciences Cancer Mutation PCR Assays
    1 SABiosciences qBiomarker Copy Number PCR Array 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, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    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

  • 20/22 diseases for SMC1A (see all 22):    About MalaCards
    smc1a-related cornelia de lange syndrome    cornelia de lange syndrome    sc phocomelia syndrome    roberts syndrome
    nijmegen breakage syndrome    ataxia telangiectasia    hypertrophic cardiomyopathy    ataxia
    intellectual disability    retinitis pigmentosa    acute myeloid leukemia    retinitis
    kaposi's sarcoma    pneumonia    mental retardation    myeloid leukemia
    tuberculosis    hypoxia    sarcoma    colorectal cancer

    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)
    About This Section

    PubMed articles for SMC1A gene, integrated from 9 sources (see all 151):
    (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. (1995)
    2. Mutations and variants in the cohesion factor genes N IPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lan ge syndrome. (PubMed id 20358602)1, 2, 4 PiAc J....Ramos F.J. (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. (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. (2003)
    5. Hypertrophic cardiomyopathy in a girl with Cornelia d e Lange syndrome due to mutation in SMC1A. (PubMed id 20635401)1, 2 Limongelli G....Larizza L. (2010)
    6. Cornelia de Lange syndrome mutations in SMC1A or SMC3 affect binding to DNA. (PubMed id 18996922)1, 2 Revenkova E....Musio A. (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. (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. (2007)
    9. X-linked Cornelia de Lange syndrome owing to SMC1L1 mutations. (PubMed id 16604071)1, 2 Musio A.... Larizza L. (2006)
    10. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 8243 HGNC: 11111 AceView: SMC1L1 Ensembl:ENSG00000072501 euGenes: HUgn8243
    ECgene: SMC1A Kegg: 8243 H-InvDB: SMC1A

    (According to HUGE)
    About This Section
    HUGE: KIAA0178

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SMC1A Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SMC1A

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

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