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

SPATA31D5P Gene

pseudogene   GIFtS: 19
GCID: GC09P084535

SPATA31 Subfamily D, Member 5, Pseudogene

(Previous names: family with sequence similarity 75, member D5, family with...)
(Previous symbol: FAM75D5)
  Search for SPATA31D5P
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

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 D, Member 5, Pseudogene1 2
FAM75D51 2
Family With Sequence Similarity 75, Member D51
Family With Sequence Similarity 75, Member D5, Pseudogene1
FAM75D5P2

External Ids:    HGNC: 386021   Entrez Gene: 3471272   Ensembl: ENSG000002406327   
ORGUL members:         
NONCODE14:n407395      

Export aliases for SPATA31D5P gene to outside databases

Previous GC identifer: GC09P084534


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

GeneCards Summary for SPATA31D5P Gene: 
SPATA31D5P (SPATA31 subfamily D, member 5, pseudogene) is a pseudogene, and is affiliated with the lncRNA class.


(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_000009.11  NC_018920.2  NT_008470.19  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SPATA31D5P
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SPATA31D5P


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

Entrez Gene cytogenetic band: 9q21.32   Ensembl cytogenetic band:  9q21.32   HGNC cytogenetic band: 9q21.32

SPATA31D5P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPATA31D5P gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P084535:  view genomic region     (about GC identifiers)

Start:
84,528,352 bp from pter      End:
84,534,842 bp from pter
Size:
6,491 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: --
Post-translational modifications:
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_

  • SPATA31D5P Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
      --

    (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

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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 SPATA31D5P

    (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
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    (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,
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    About This Section

    REFSEQ mRNAs for SPATA31D5P gene: 
    NM_198509.1  

    Unigene Cluster for SPATA31D5P:

    SPATA31 subfamily D, member 5, pseudogene
    Hs.215235  [show with all ESTs]
    Unigene Representative Sequence: AK128229
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000527857(uc011lst.2) ENST00000376459
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    Additional mRNA sequence: 

    AK125938.1 AK128229.1 BC104780.1 BC104782.1 NR_026851.1 XR_159520.1 

    3 DOTS entries:

    DT.453716  DT.101983140  DT.101983139 

    7 AceView cDNA sequences:

    AK125938 BX096267 AA609730 AA725800 AK128229 BV195301 BG772383 

    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™, 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
    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --


    SOURCE GeneReport for Unigene cluster: Hs.215235
        SABiosciences Custom PCR Arrays for SPATA31D5P
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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)
    About This Section
      --

    ENSEMBL Gene Tree for SPATA31D5P (if available)
    TreeFam Gene Tree for SPATA31D5P (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    7 SNPs in SPATA31D5P are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1911483791,2
    C,F--84533976(+) GTGGAG/CGGGAT 1 -- nc-transcript-variant1Minor allele frequency- C:0.01EU 575
    rs2018170911,2
    F--84533988(+) CAGGGC/TTGGGG 1 -- nc-transcript-variant1Minor allele frequency- T:0.01EU 467
    rs2009292681,2
    F--84534345(+) GTCCCT/CAAGAA 1 -- nc-transcript-variant1Minor allele frequency- C:0.01EU 577
    rs1997374381,2
    ----84533872(+) GGAGCA/CCAGGG 1 -- nc-transcript-variant1Minor allele frequency- C:0.00EU 551
    rs1997896461,2
    ----84534106(+) CCTTTT/CCAGAA 1 -- nc-transcript-variant1Minor allele frequency- C:0.00EU 567
    rs3724857791,2
    ----84526354(+) TTTAGC/TCAGGC 1 -- us2k10--------
    rs3740735311,2
    ----84528614(+) TTGTT-/GTTTCCCA 1 -- int10--------

    HapMap Linkage Disequilibrium report for SPATA31D5P (84528352 - 84534842 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SPATA31D5P: --
    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing SPATA31D5P
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    (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
      --

    (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 SPATA31D5P gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SPATA31D5P)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 347127 HGNC: 38602 AceView: FLJ43950 Ensembl:ENSG00000240632 euGenes: HUgn347127
    ECgene: SPATA31D5P H-InvDB: SPATA31D5P

    (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
      --

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SPATA31D5P gene:
    Search GeneIP for patents involving SPATA31D5P

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



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