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

SLIRP Gene

protein-coding   GIFtS: 47
GCID: GC14P078175

SRA Stem-Loop Interacting RNA Binding Protein

(Previous name: chromosome 14 open reading frame 156)
(Previous symbol: C14orf156)
  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
SRA Stem-Loop Interacting RNA Binding Protein1 2
C14orf1561 2 3 5
Chromosome 14 Open Reading Frame 1561
DC502
PD048722
SRA Stem-Loop-Interacting RNA-Binding Protein, Mitochondrial2

External Ids:    HGNC: 204951   Entrez Gene: 818922   Ensembl: ENSG000001197057   OMIM: 6102115   UniProtKB: Q9GZT33   

Export aliases for SLIRP gene to outside databases


(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 SLIRP Gene:
Steroid receptor RNA activator (SRA, or SRA1; MIM 603819) is a complex RNA molecule containing multiple stable
stem-loop structures that functions in coactivation of nuclear receptors. SLIRP interacts with stem-loop
structure-7 of SRA (STR7) and modulates nuclear receptor transactivation (Hatchell et al., 2006 (PubMed
16762838)).(supplied by OMIM, Mar 2008)

GeneCards Summary for SLIRP Gene: 
SLIRP (SRA stem-loop interacting RNA binding protein) is a protein-coding gene. Diseases associated with SLIRP include thyroiditis, and gastric cancer. GO annotations related to this gene include RNA binding and nucleotide binding.

UniProtKB/Swiss-Prot: SLIRP_HUMAN, Q9GZT3
Function: RNA-binding protein that acts as a nuclear receptor corepressor. Probably acts by binding the SRA RNA,
and repressing the SRA-mediated nuclear receptor coactivation. Binds the STR7 loop of SRA RNA. Also able to
repress glucocorticoid (GR), androgen (AR), thyroid (TR) and VDR-mediated transactivation




(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_000014.8  NC_018925.2  NT_026437.12  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SLIRP
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLIRP promoter sequence
   Search SABiosciences Chromatin IP Primers for SLIRP

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


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

Entrez Gene cytogenetic band: 14q24.3   Ensembl cytogenetic band:  14q24.3   HGNC cytogenetic band: 14q24.3

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

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14P078175:  view genomic region     (about GC identifiers)

Start:
78,174,414 bp from pter      End:
78,227,447 bp from pter
Size:
53,034 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: SLIRP_HUMAN, Q9GZT3 (See protein sequence)
Recommended Name: SRA stem-loop-interacting RNA-binding protein, mitochondrial precursor  
Size: 109 amino acids; 12349 Da
Subcellular location: Mitochondrion. Nucleus. Note=Predominantly mitochondrial. Some fraction is nuclear. In the
nucleus, it is recruited to nuclear receptor target promoters
Secondary accessions: J3KMY7
Alternative splicing: 2 isoforms:  Q9GZT3-1   Q9GZT3-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SLIRP: NX_Q9GZT3

Explore proteomics data for SLIRP at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9GZT3

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

    SLIRP Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001254792.1  NP_001254793.1  NP_112487.1  

    ENSEMBL proteins: 
     ENSP00000450909   ENSP00000238688   ENSP00000452057   ENSP00000450849   ENSP00000451606  
     ENSP00000450770   ENSP00000452162   ENSP00000452329   ENSP00000450587  

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    Cloud-Clone Corp. Proteins for SLIRP 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005739mitochondrion IDA--
    GO:0030529ribonucleoprotein complex IEA--

    SLIRP 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: 
    RBM: RNA binding motif (RRM) containing

    2 InterPro protein domains:
     IPR000504 RRM_dom
     IPR012677 Nucleotide-bd_a/b_plait

    Graphical View of Domain Structure for InterPro Entry Q9GZT3

    ProtoNet protein and cluster: Q9GZT3

    1 Blocks protein domain: IPB000504 RNA-binding region RNP-1 (RNA recognition motif)

    UniProtKB/Swiss-Prot: SLIRP_HUMAN, Q9GZT3
    Similarity: Contains 1 RRM (RNA recognition motif) domain


    SLIRP 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: SLIRP_HUMAN, Q9GZT3
    Function: RNA-binding protein that acts as a nuclear receptor corepressor. Probably acts by binding the SRA RNA,
    and repressing the SRA-mediated nuclear receptor coactivation. Binds the STR7 loop of SRA RNA. Also able to
    repress glucocorticoid (GR), androgen (AR), thyroid (TR) and VDR-mediated transactivation

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding IEA--
         
    SLIRP for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for SLIRP 
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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 SLIRP

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

    5/255 Interacting proteins for SLIRP (Q9GZT32, 3 ENSP000002386884) via UniProtKB, MINT, STRING, and/or I2D (see all 255)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ICT1Q141972, 3, ENSP000003015854MINT-8079030 I2D: score=1 STRING: ENSP00000301585
    SLX1AQ9BQ833, ENSP000002513034I2D: score=2 STRING: ENSP00000251303
    SLX1BQ9BQ833, ENSP000003289404I2D: score=2 STRING: ENSP00000328940
    LRPPRCP427042, ENSP000002606654MINT-8340644 MINT-8079030 STRING: ENSP00000260665
    BABAM1Q9NWV83, ENSP000003524084I2D: score=2 STRING: ENSP00000352408
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000961negative regulation of mitochondrial RNA catabolic process IEA--
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent IEA--

    SLIRP 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 SLIRP

    Search CenterWatch for drugs/clinical trials and news about SLIRP

    (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 SLIRP gene (3 alternative transcripts): 
    NM_001267863.1  NM_001267864.1  NM_031210.5  

    Unigene Cluster for SLIRP:

    SRA stem-loop interacting RNA binding protein
    Hs.655105  [show with all ESTs]
    Unigene Representative Sequence: BQ278491
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000557342(uc001xue.4) ENST00000238688 ENST00000557623 ENST00000557431
    ENST00000555890 ENST00000556831 ENST00000554074 ENST00000556375 ENST00000556310
    ENST00000553981 ENST00000556956
    miRNA
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    Additional mRNA sequence: 

    AF253980.1 AF271779.1 AJ272055.1 AY860853.1 BC017895.1 NR_052025.1 

    16 DOTS entries:

    DT.101959452  DT.205936  DT.116858  DT.101983692  DT.120787428  DT.92412491  DT.92430511  DT.101983691 
    DT.100793671  DT.75174198  DT.100030853  DT.116859  DT.120787377  DT.120787404  DT.120787439  DT.95308927 

    24/267 AceView cDNA sequences (see all 267):

    BQ777999 BM661888 F35313 AA524049 F34894 F20520 AA926970 AA694164 
    AA780729 AA534561 BU070427 BU726271 AI911004 BQ614067 AI130748 AA694524 
    AA864997 AA541603 AI309287 AA927025 BU070572 AA905241 BM661754 BE049640 

    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

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


    SLIRP expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/26 selected tissues (see all 26) fully expand
     
     Testis (Reproductive System)    fully expand to see all 3 entries
             Leydig Cells Testis Interstitium
             testis ; cells in seminiferus ducts   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 3 entries
             colon ; peripheral nerve/ganglion   
     
     Tonsil (Hematopoietic System)    fully expand to see all 3 entries
             tonsil ; squamous epithelial cells   
     
     Epithelium (Uncategorized)    fully expand to see all 3 entries
             oral mucosa ; squamous epithelial cells   
     
     Uterus (Reproductive System)    fully expand to see all 2 entries
             uterus, post-menopause ; glandular cells   

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

    SOURCE GeneReport for Unigene cluster: Hs.655105

    UniProtKB/Swiss-Prot: SLIRP_HUMAN, Q9GZT3
    Tissue specificity: Ubiquitously expressed, with highest level in heart, liver, skeletal muscle and testis

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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

    This gene was present in the common ancestor of animals.

    Orthologs for SLIRP gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slirp1 , 5 RIKEN cDNA 1810035L17 gene5
    SRA stem-loop interacting RNA binding protein1
    78.62(n)1
    71.7(a)1
      12 (41.67 cM)5
    3807731  NM_026958.31  NP_081234.21 
     874438965 
    chicken
    (Gallus gallus)
    Aves SLIRP1 SRA stem-loop interacting RNA binding protein 53.7(n)
    47.78(a)
      772054  XM_001235248.2  XP_001235249.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sb:cb6571 sb:cb657 62.88(n)
    55.68(a)
      368358  XM_002665165.2  XP_002665211.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG337146
    CG80216
    --
    31(a)
    30(a)
    many → 1
    many → 1
    X(21188961-21190299)
    3R(4476806-4477215)
    worm
    (Caenorhabditis elegans)
    Secernentea C50B8.16
    Protein C50B8.1
    24(a)
    1 ↔ 1
    V(13565861-13566958)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SLIRP gene
    9 SIMAP similar genes for SLIRP using alignment to 8 protein entries:     SLIRP_HUMAN (see all proteins):
    HNRNPD    DAZAP1    HNRNPAB    MSI2    HNRNPA0    TARDBP
    RBM28    DAZAP1/MEF2D fusion    PABPN1

    SLIRP for paralogs           About GeneDecksing


    4 Pseudogenes.org Pseudogenes for SLIRP
    PGOHUM00000261863 PGOHUM00000261879 PGOHUM00000245481 PGOHUM00000242066


    (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

    10/179 SNPs in SLIRP are shown (see all 179)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1893395761,2
    --78176408(+) ATATTA/GTAAAA 4 -- int10--------
    rs788092091,2
    C--78176596(+) AAGGAC/TAGTTA 4 -- int10--------
    rs791881711,2
    F--78176640(+) TACCAA/GCATAT 4 -- int11Minor allele frequency- G:0.02WA 118
    rs1821788671,2
    --78176644(+) AACATA/GTGGAG 4 -- int10--------
    rs1384320511,2
    --78176683(+) AACCCA/GCAGGA 4 -- int10--------
    rs1176989401,2
    C,F--78176706(+) ATTCAA/GTTAGT 4 -- int11Minor allele frequency- G:0.03NA 120
    rs748335161,2
    F--78176755(+) AGGCAG/CGAAGG 4 -- int11Minor allele frequency- C:0.02WA 118
    rs10778431,2
    C,H--78176789(-) ATTTAG/ATAAAA 4 -- int18Minor allele frequency- A:0.06NA EA NS 652
    rs10764961,2
    C,F,H--78176851(-) CAGTGT/CGTTTC 4 -- int128Minor allele frequency- C:0.44EA NA NS WA CSA 3068
    rs1164317741,2
    C,F--78176976(+) ACTCAA/GCAACT 4 -- int1 nc-transcript-variant1Minor allele frequency- G:0.03WA 118

    HapMap Linkage Disequilibrium report for SLIRP (78174414 - 78227447 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for SLIRP:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv521287CNV Gain19592680
    esv34940CNV Gain17911159
    nsv520021CNV Gain19592680
    essv7944CNV CNV17122850
    dgv643e1CNV Complex17122850

    SABiosciences Cancer Mutation PCR Assays
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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
    OMIM gene information: 610211    OMIM disorders: --

    2 diseases for SLIRP:    About MalaCards
    thyroiditis    gastric cancer


    SLIRP for disorders           About GeneDecksing


    Export disorders for SLIRP 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 SLIRP gene, integrated from 9 sources (see all 28):
    (articles sorted by number of sources associating them with SLIRP)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. SLIRP, a small SRA binding protein, is a nuclear receptor corepressor. (PubMed id 16762838)1, 2, 3 Hatchell E.C.... Leedman P.J. (2006)
    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. (2004)
    3. Interlaboratory reproducibility of large-scale human p rotein-complex analysis by standardized AP-MS. (PubMed id 23455922)1 Varjosalo M....Superti-Furga G. (2013)
    4. Novel, gel-free proteomics approach identifies RNF5 an d JAMP as modulators of GPCR stability. (PubMed id 23798571)1 Roy S.J....Parent J.L. (2013)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. Global landscape of HIV-human protein complexes. (PubMed id 22190034)1 Jager S....Krogan N.J. (2012)
    7. LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria. (PubMed id 22661577)1 Chujo T....Suzuki T. (2012)
    8. A bead-based approach for large-scale identification o f in vitro kinase substrates. (PubMed id 22113938)1 Zhang M....Zou H. (2011)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    10. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 81892 HGNC: 20495 AceView: C14orf156 Ensembl:ENSG00000119705 euGenes: HUgn81892
    ECgene: SLIRP H-InvDB: SLIRP

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for SLIRP Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for SLIRP gene:
    Search GeneIP for patents involving SLIRP

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