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SIRPD Gene

protein-coding   GIFtS: 42
GCID: GC20M001514

Signal-Regulatory Protein Delta

(Previous names: protein tyrosine phosphatase, non-receptor type substrate...)
(Previous symbol: PTPNS1L2)
  Search for SIRPD
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
Signal-Regulatory Protein Delta1 2
PTPNS1L21 2 3
Protein Tyrosine Phosphatase, Non-Receptor Type Substrate 1-Like 21 2
Protein Tyrosine Phosphatase Non-Receptor Type Substrate 1-Like 22 3
SIRP-delta2 3
dJ576H24.42

External Ids:    HGNC: 162481   Entrez Gene: 1286462   Ensembl: ENSG000001259007   UniProtKB: Q9H1063   

Export aliases for SIRPD gene to outside databases

Previous GC identifers: GC20M001463 GC20M001465


(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 SIRPD Gene:
SIRPD (signal-regulatory protein delta) is a protein-coding gene. An important paralog of this gene is SIRPB2.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the SIRPD gene promoter:
         GCNF   HTF   XBP-1   Max   GCNF-1   GCNF-2   c-Myc   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSIRPD promoter sequence
   Search Chromatin IP Primers for SIRPD

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


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

Entrez Gene cytogenetic band: 20p13   Ensembl cytogenetic band:  20p13   HGNC cytogenetic band: 20p13

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

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M001514:  view genomic region     (about GC identifiers)

Start:
1,514,897 bp from pter      End:
1,539,489 bp from pter
Size:
24,593 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: SIRPD_HUMAN, Q9H106 (See protein sequence)
Recommended Name: Signal-regulatory protein delta precursor  
Size: 197 amino acids; 21687 Da
Secondary accessions: B3KS88 Q5TFQ6

Explore the universe of human proteins at neXtProt for SIRPD: NX_Q9H106

Explore proteomics data for SIRPD at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn174

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

    REFSEQ proteins: NP_848555.2  
    ENSEMBL proteins: 
     ENSP00000410072   ENSP00000371034   ENSP00000371036  

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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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    HGNC Gene Families:
    SIRP: Signal-regulatory proteins
    VSET: Immunoglobulin superfamily / V-set domain containing

    4 InterPro protein domains:
     IPR013783 Ig-like_fold
     IPR013106 Ig_V-set
     IPR007110 Ig-like_dom
     IPR003599 Ig_sub

    Graphical View of Domain Structure for InterPro Entry Q9H106

    ProtoNet protein and cluster: Q9H106

    1 Blocks protein domain: IPB003599 Immunoglobulin subtype

    UniProtKB/Swiss-Prot: SIRPD_HUMAN, Q9H106
    Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain


    SIRPD 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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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    SIRPD for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SIRPD:
     Proliferating cells 

    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
    SIRPD_HUMAN, Q9H106: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    plasma membrane3
    cytosol1
    endoplasmic reticulum1
    mitochondrion1
    nucleus1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

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

        Search GeneGlobe Interaction Network for SIRPD

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

    Selected Interacting proteins for SIRPD (ENSP000003710364) via UniProtKB, MINT, STRING, and/or I2D (see all 32)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CD8BENSP000003311724STRING: ENSP00000331172
    LYZENSP000002612674STRING: ENSP00000261267
    SIRPAENSP000003483074STRING: ENSP00000348307
    CD4ENSP000000116534STRING: ENSP00000011653
    IGHEENSP000003749834STRING: ENSP00000374983
    About this table

    (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 SIRPD



    (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 SIRPD gene: 
    NM_178460.2  

    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000429387 ENST00000381621 ENST00000381623(uc002wfi.3)
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    Selected AceView cDNA sequences (see all 67):

    BQ635329 AA709221 BQ635330 CD369292 AL597487 BM285386 BQ635331 AK130124 
    BI756472 CA748838 BC025286 AI201145 BM010247 AI088704 AX747909 CD742880 
    BC075835 NM_178460 BI823904 AI219993 BQ027400 T78888 BI910932 BI518525 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SIRPD    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5 ^ 6
    SP1:                                      -               
    SP2:                                      -               
    SP3:        -                                             
    SP4:                                                      


    ECgene alternative splicing isoforms for SIRPD

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


    SIRPD expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Blood (Hematopoietic System)
             Granulocytes Peripheral Blood
     
     Testis (Reproductive System)
    SIRPD Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SIRPD Protein Expression
        Custom PCR Arrays for SIRPD
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SIRPD

    (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 chordates.

    Orthologs for SIRPD gene from Selected species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia SIRPD6
    signal-regulatory protein delta
    34(a)
    1 ↔ 1
    24(19451330-19459630)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    32(a)
    1 → many
    GL343515.1(139492-140536)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SIRPD gene
    SIRPB22  SIRPB12  SIRPG2  SIRPA2  ENSG000002608612  
    4 SIMAP similar genes for SIRPD using alignment to 3 protein entries:     SIRPD_HUMAN (see all proteins):
    SIRPB1    SIRPG    PTPNS1    SIRPB2

    SIRPD 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 SIRPD (see all 642)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1467191711,2
    --1514397(+) ACGGAC/TTTCTC 1 -- int10--------
    rs1158281281,2
    C,F--1514455(+) CACACG/ATCAGC 1 -- int11Minor allele frequency- A:0.01WA 118
    rs746475321,2
    F--1514484(+) ATGAGG/ACTGCG 1 -- int11Minor allele frequency- A:0.05WA 118
    rs1896118301,2
    --1514488(+) GGCTGA/CGGTCC 1 -- int10--------
    rs735691221,2
    C--1514554(+) ATGTAT/CTAGCT 1 -- int12Minor allele frequency- C:0.04WA 120
    rs1488587671,2
    --1514626(+) CAGCCC/TTTGCT 1 -- int10--------
    rs1815391311,2
    --1514787(+) CGCAGC/GTTTCA 1 -- int10--------
    rs1434923401,2
    --1514810(+) TAGAGA/CACATT 1 -- int10--------
    rs1509428071,2
    --1514959(+) TGGAAG/TAAAGC 1 -- ut310--------
    rs1998624241,2
    --1515030(+) TATGGA/GGGCTT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SIRPD (1514897 - 1539489 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for SIRPD:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv833893CNV Loss17160897
    nsv510779CNV Loss20534489
    nsv9775CNV Loss18304495
    nsv428374CNV Loss18775914
    dgv4516n71CNV Gain21882294
    nsv522008CNV Gain19592680
    nsv833894CNV Gain17160897
    dgv1302e1CNV Complex17122850
    dgv1301e1CNV Complex17122850

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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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    SIRPD for disorders           About GeneDecksing

    Genetic Association Database (GAD): SIRPD
    Human Genome Epidemiology (HuGE) Navigator: SIRPD (1 document)

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

    1. A nomenclature for signal regulatory protein family members. (PubMed id 16339511)1, 3 van den Berg T.K....Barclay A.N. (J. Immunol. 2005)
    2. 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. (Genome Res. 2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
    5. Genome-wide YFP fluorescence complementation screen identifies new regulators for telomere signaling in human cells. (PubMed id 21044950)1 Lee O.H....Songyang Z. (amp 2011)
    6. Single-nucleotide polymorphisms, acute rejection, and severity of tubulitis in kidney transplantation, accounting for center-to-center variation. (PubMed id 21085059)4 Israni A....Oetting W.S. (Transplantation 2010)
    7. 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)
    8. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 128646 HGNC: 16248 AceView: SIRPB1andPTPNS1L2 Ensembl:ENSG00000125900 euGenes: HUgn128646
    ECgene: SIRPD H-InvDB: SIRPD

    (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 SIRPD 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 SIRPD gene:
    Search GeneIP for patents involving SIRPD

    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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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