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

SCML1 Gene

protein-coding   GIFtS: 43
GCID: GC0XP017755

Sex Comb On Midleg-Like 1 (Drosophila)

(Previous name: sex comb on midleg (Drosophila)-like 1)
  Search for SCML1
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
Sex Comb On Midleg-Like 1 (Drosophila)1 2
Sex Comb On Midleg (Drosophila)-Like 11
Sex Comb On Midleg-Like Protein 12

External Ids:    HGNC: 105801   Entrez Gene: 63222   Ensembl: ENSG000000476347   OMIM: 3002275   UniProtKB: Q9UN303   

Export aliases for SCML1 gene to outside databases

Previous GC identifers: GC0XP017299 GC0XP016421 GC0XP016957 GC0XP017117 GC0XP017515 GC0XP017665 GC0XP015514


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

GeneCards Summary for SCML1 Gene: 
SCML1 (sex comb on midleg-like 1 (Drosophila)) is a protein-coding gene. GO annotations related to this gene include DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is L3MBTL1.

UniProtKB/Swiss-Prot: SCML1_HUMAN, Q9UN30
Function: Putative Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are
required to maintain the transcriptionally repressive state of homeotic genes throughout development. May be
involved in spermatogenesis during sexual maturation (By similarity)




(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  NT_167197.1  NC_018934.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SCML1 gene promoter:
         Pax-2   Pax-2a   LUN-1   YY1   Evi-1   HEN1   POU2F1   POU2F1a   aMEF-2   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCML1 promoter sequence
   Search SABiosciences Chromatin IP Primers for SCML1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCML1


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

Entrez Gene cytogenetic band: Xp22   Ensembl cytogenetic band:  Xp22.13   HGNC cytogenetic band: Xp22

SCML1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCML1 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP017755:  view genomic region     (about GC identifiers)

Start:
17,755,588 bp from pter      End:
17,773,105 bp from pter
Size:
17,518 bases      Orientation:
plus 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: SCML1_HUMAN, Q9UN30 (See protein sequence)
Recommended Name: Sex comb on midleg-like protein 1  
Size: 329 amino acids; 37447 Da
Subcellular location: Nucleus (Probable)
Secondary accessions: B0FZN6 B2RA08 Q5H968 Q5H969
Alternative splicing: 3 isoforms:  Q9UN30-3   Q9UN30-1   Q9UN30-2   

Explore the universe of human proteins at neXtProt for SCML1: NX_Q9UN30

Explore proteomics data for SCML1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9UN30

  • SCML1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SCML1 Protein Expression
    REFSEQ proteins (4 alternative transcripts): 
    NP_001032624.1  NP_001032625.1  NP_001032629.1  NP_006737.2  

    ENSEMBL proteins: 
     ENSP00000369384   ENSP00000369380   ENSP00000369382   ENSP00000392587   ENSP00000381154  

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    Cloud-Clone Corp. Proteins for SCML1 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    SCML1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    SAMD: Sterile alpha motif (SAM) domain containing

    3 InterPro protein domains:
     IPR013761 SAM/pointed
     IPR001660 SAM
     IPR021129 SAM_type1

    Graphical View of Domain Structure for InterPro Entry Q9UN30

    ProtoNet protein and cluster: Q9UN30

    1 Blocks protein domain: IPB001660 Sterile alpha motif SAM

    UniProtKB/Swiss-Prot: SCML1_HUMAN, Q9UN30
    Similarity: Belongs to the SCM family
    Similarity: Contains 1 SAM (sterile alpha motif) domain


    SCML1 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: SCML1_HUMAN, Q9UN30
    Function: Putative Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are
    required to maintain the transcriptionally repressive state of homeotic genes throughout development. May be
    involved in spermatogenesis during sexual maturation (By similarity)

         Genatlas biochemistry entry for SCML1:
    Drosophila sex comb on midleg-like 1 homolog,polycomb group (PcG),involved in transcriptional repression of HOX
    genes

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding TAS9570953
    GO:0003700sequence-specific DNA binding transcription factor activity TAS9570953
    GO:0005515protein binding ----
         
    SCML1 for ontologies           About GeneDecksing


    Animal Models:
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SCML1 
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    hsa-miR-3163 hsa-miR-2052 hsa-miR-19b-2* hsa-miR-153 hsa-miR-659 hsa-miR-19b-1* hsa-miR-19a* hsa-miR-24
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    (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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCML1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    5/7 Interacting proteins for SCML1 (ENSP000003693804) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CBX2ENSP000003087504STRING: ENSP00000308750
    PCGF2ENSP000003540334STRING: ENSP00000354033
    PHC2ENSP000002571184STRING: ENSP00000257118
    RNF2ENSP000003564804STRING: ENSP00000356480
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0009653anatomical structure morphogenesis TAS9570953

    SCML1 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
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SCML1

    Search CenterWatch for drugs/clinical trials and news about SCML1

    (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 SCML1 gene (4 alternative transcripts): 
    NM_001037535.2  NM_001037536.2  NM_001037540.2  NM_006746.5  

    Unigene Cluster for SCML1:

    Sex comb on midleg-like 1 (Drosophila)
    Hs.109655  [show with all ESTs]
    Unigene Representative Sequence: NM_001037540
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000380045(uc004cyd.3) ENST00000380041 ENST00000380043(uc004cyb.3 uc004cyc.3 uc004cye.3)
    ENST00000427362 ENST00000419185 ENST00000487842 ENST00000398080
    miRNA
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    8 QIAGEN miScript miRNA Assays for microRNAs that regulate SCML1:
    hsa-miR-3163 hsa-miR-2052 hsa-miR-19b-2* hsa-miR-153 hsa-miR-659 hsa-miR-19b-1* hsa-miR-19a* hsa-miR-24
    SwitchGear 3'UTR luciferase reporter plasmidSCML1 3' UTR sequence
    Inhib. RNA
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SCML1

    Additional mRNA sequence: 

    AF160728.1 AK313993.1 BC009193.2 BC026159.2 BC105028.1 

    11 DOTS entries:

    DT.100748552  DT.95369106  DT.310945  DT.95251213  DT.86999637  DT.92437725  DT.95369117  DT.92437739 
    DT.121278083  DT.412147  DT.95317901 

    24/160 AceView cDNA sequences (see all 160):

    BX509468 AW955389 CB243357 CD742734 BF431992 NM_006746 CD370105 CK822373 
    BU193823 AI269405 AI537061 AI431345 BM141950 AV728506 AW593093 BC026159 
    AA304825 BF059263 AV719246 W69459 BM352062 AL705642 BE794092 AI978764 

    GeneLoc Exon Structure

    5/10 Alternative Splicing Database (ASD) splice patterns (SP) for SCML1 (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11
    SP1:                                -     -     -                                                                     
    SP2:                                -     -     -           -                                                         
    SP3:                                -     -     -           -                                                         
    SP4:                                -     -     -     -     -                                                         
    SP5:                                -     -     -     -     -                                                         


    ECgene alternative splicing isoforms for SCML1

    (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

    SCML1 expression in normal human tissues (normalized intensities)      SCML1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCATAAGATT
    SCML1 Expression
    About this image


    SCML1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/4 selected tissues (see all 4) fully expand
     
     Blood (Cardiovascular System)    fully expand to see all 4 entries
             T Helper Cells Thymus
             cd31+ cells   
     
     Thymus (Hematopoietic System)    fully expand to see all 2 entries
             T Helper Cells Thymus
     
     Endothelium (Cardiovascular System)
             cd31+ cells   
     
     Testis (Reproductive System)

    See SCML1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SCML1

    SOURCE GeneReport for Unigene cluster: Hs.109655

    UniProtKB/Swiss-Prot: SCML1_HUMAN, Q9UN30
    Tissue specificity: Ubiquitous. Expressed in fetal and adult tissues

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCML1

    (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 mammals.

    Orthologs for SCML1 gene from 1/3 species (see all 3)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia SCML11 sex comb on midleg-like 1 (Drosophila) 68.42(n)
    56.04(a)
      491758  XM_548878.3  XP_548878.3 


    ENSEMBL Gene Tree for SCML1 (if available)
    TreeFam Gene Tree for SCML1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SCML1 gene
    L3MBTL12  L3MBTL22  SCML42  L3MBTL32  SFMBT12  L3MBTL42  SCMH12  SCML22  
    SFMBT22  MBTD12  

    SCML1 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

    10/191 SNPs in SCML1 are shown (see all 191)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs736366641,2
    C,F--17754661(+) GCCTCC/GATATA 4 -- us2k11Minor allele frequency- G:0.00WA 2
    rs1822847291,2
    --17754937(+) TGCTGA/GAGACT 4 -- us2k10--------
    rs1409662181,2
    C--17754939(+) CTGGAA/GACTGG 4 -- us2k10--------
    rs1849606711,2
    --17755111(+) GCGGGA/GGAGGG 4 -- us2k10--------
    rs1147086941,2
    C--17755181(+) CCACGA/TCCCTA 4 -- us2k10--------
    rs1830802251,2
    --17755278(+) CCTAAC/TGTCCA 4 -- us2k10--------
    rs1129731201,2
    C,F--17755296(+) TCCTGA/CGGGTC 4 -- us2k11Minor allele frequency- C:0.00CSA 1
    rs1931976901,2
    --17755343(+) ACAGCC/TATCTC 4 -- us2k10--------
    rs780305431,2
    C--17755535(+) GCGGGA/TAGTCC 4 -- us2k10--------
    rs1833665421,2
    --17755840(+) TTTCCA/GTCACG 4 -- int10--------

    HapMap Linkage Disequilibrium report for SCML1 (17755588 - 17773105 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SCML1: --
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing SCML1
    DNA2.0 Custom Variant and Variant Library Synthesis for SCML1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SCML1 for disorders           About MalaCards
    OMIM gene information: 300227    OMIM disorders: --


    SCML1 for disorders           About GeneDecksing


    Export disorders for SCML1 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 SCML1 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with SCML1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of SCML1, a new gene in Xp22, with homology to developmental polycomb genes. (PubMed id 9570953)1, 2, 3 van de Vosse E....Trump D. (1998)
    2. Adaptive evolution of SCML1 in primates, a gene involved in male reproduction. (PubMed id 18601738)1, 2 Wu H.-H. and Su B. (2008)
    3. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (2005)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    5. Interlaboratory reproducibility of large-scale human p rotein-complex analysis by standardized AP-MS. (PubMed id 23455922)1 Varjosalo M....Superti-Furga G. (2013)
    6. PCGF homologs, CBX proteins, and RYBP define functiona lly distinct PRC1 family complexes. (PubMed id 22325352)1 Gao Z....Reinberg D. (2012)
    7. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    8. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. (PubMed id 18691976)2 Daub H.... Mann M. (2008)
    9. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6322 HGNC: 10580 AceView: SCML1 Ensembl:ENSG00000047634 euGenes: HUgn6322
    ECgene: SCML1 H-InvDB: SCML1

    (According to HUGE)
    About This Section
      --

    (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 SCML1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SCML1 gene:
    Search GeneIP for patents involving SCML1

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



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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