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SPATA31C1 Gene

pseudogene   GIFtS: 26
GCID: GC09P090529

SPATA31 Subfamily C, Member 1

(Previous names: family with sequence similarity 75, member C1)
(Previous symbol: FAM75C1)
  Search for SPATA31C1
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
SPATA31 Subfamily C, Member 11 2
FAM75C11 2 3
Family With Sequence Similarity 75, Member C11 2
SPATA31C22
Spermatogenesis-Associated Protein 31C22
Protein FAM75C13

External Ids:    HGNC: 278461   Entrez Gene: 4414522   Ensembl: ENSG000002302467   UniProtKB: P0DKV03   
ORGUL members:         

Export aliases for SPATA31C1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SPATA31C1 Gene:
SPATA31C1 (SPATA31 subfamily C, member 1) is a pseudogene, and is affiliated with the lncRNA class.

UniProtKB/Swiss-Prot: S31C1_HUMAN, P0DKV0
Function: May play a role in spermatogenesis (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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SPATA31C1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPATA31C1


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

Entrez Gene cytogenetic band: 9q22   Ensembl cytogenetic band:  9q22.1   HGNC cytogenetic band: 9q22.1

SPATA31C1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPATA31C1 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P090529:  view genomic region     (about GC identifiers)

Start:
90,529,408 bp from pter      End:
90,538,572 bp from pter
Size:
9,165 bases      Orientation:
plus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: S31C1_HUMAN, P0DKV0 (See protein sequence)
Recommended Name: Spermatogenesis-associated protein 31C1  
Size: 1188 amino acids; 130522 Da
Alternative splicing: 2 isoforms:  P0DKV0-1   P0DKV0-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SPATA31C1: NX_P0DKV0

Explore proteomics data for SPATA31C1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SPATA31C1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001138596.1  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR027970 DUF4599

    Graphical View of Domain Structure for InterPro Entry P0DKV0

    ProtoNet protein and cluster: P0DKV0

    UniProtKB/Swiss-Prot: S31C1_HUMAN, P0DKV0
    Similarity: Belongs to the SPATA31 family


    Find genes that share domains with SPATA31C1           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: S31C1_HUMAN, P0DKV0
    Function: May play a role in spermatogenesis (By similarity)

    Animal Models:

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    (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
    S31C1_HUMAN, P0DKV0: Membrane; Single-pass membrane protein (Potential)

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with SPATA31C1           About GenesLikeMe


    (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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SPATA31C1
    Interactions:

        Search GeneGlobe Interaction Network for SPATA31C1

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007283spermatogenesis IEA--
    GO:0030154cell differentiation IEA--

    Find genes that share ontologies with SPATA31C1           About GenesLikeMe



    (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
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    Browse Tocris compounds for SPATA31C1 (S31C1)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SPATA31C1 gene: 
    NM_001145124.1  

    Unigene Cluster for SPATA31C1:

    SPATA31 subfamily C, member 1
    Hs.652956  [show with all ESTs]
    Unigene Representative Sequence: NM_001145124
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000602681 ENST00000420021 ENST00000437823(uc004apq.4 uc010mqi.3)

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    Additional mRNA sequence: AK093374.1 

    3 DOTS entries:

    DT.102821944  DT.121184006  DT.121184014 

    4 AceView cDNA sequences:

    AA403176 AL080179 BX107440 AA398236 

    GeneLoc Exon Structure


    (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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    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --

    SPATA31C1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SPATA31C1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.652956
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    In Situ
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    (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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      --

    ENSEMBL Gene Tree for SPATA31C1 (if available)
    TreeFam Gene Tree for SPATA31C1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SPATA31C1 gene
    11 SIMAP similar genes for SPATA31C1 using alignment to 1 protein entry:     S31C1_HUMAN:
    DKFZp434M131    SPATA31C2    SPATA31B1    FAM75A2    SPATA31A1    SPATA31A2
    SPATA31A3    SPATA31A4    SPATA31A5    SPATA31A6    SPATA31A7

    Find genes that share paralogs with SPATA31C1           About GenesLikeMe



    (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 SPATA31C1 (see all 165)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2006014721,2
    C--90531338(+) CCTGCA/GTAAGA 1 -- us2k10--------
    rs2013774251,2
    C--90531535(+) GGATAG/TATTGA 1 -- us2k10--------
    rs1402583681,2
    C--90531561(+) TAAAAA/TAACTT 1 -- us2k10--------
    rs3692256651,2
    C--90531723(+) CTGGCC/TACACG 1 -- us2k10--------
    rs1408842291,2
    C--90531728(+) TAACAC/TGGTGA 1 -- us2k10--------
    rs3696491731,2
    C--90531911(+) CATCT-/AAAAAG 1 -- us2k10--------
    rs2004903511,2
    C--90531932(+) CTGCAG/TGTCCT 1 -- us2k10--------
    rs1876686891,2
    --90531991(+) ATTTTA/TAAAAA 1 -- us2k10--------
    rs3745367671,2
    C--90532030(+) TGATTC/GAAGTG 1 -- us2k10--------
    rs1925828411,2
    C--90532115(+) AGGTCA/CGGAGA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SPATA31C1 (90529408 - 90538572 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SPATA31C1: --
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing SPATA31C1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (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 SPATA31C1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SPATA31C1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    3. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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: 441452 HGNC: 27846 AceView: LOC441452 Ensembl:ENSG00000230246 euGenes: HUgn441452
    ECgene: SPATA31C1 H-InvDB: SPATA31C1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SPATA31C1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SPATA31C1 gene:
    Search GeneIP for patents involving SPATA31C1

    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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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