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SLIRP SRA stem-loop interacting RNA binding protein [ Homo sapiens (human) ]

Gene ID: 81892, updated on 17-Jun-2019

Summary

Official Symbol
SLIRPprovided by HGNC
Official Full Name
SRA stem-loop interacting RNA binding proteinprovided by HGNC
Primary source
HGNC:HGNC:20495
See related
Ensembl:ENSG00000119705 MIM:610211
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DC50; PD04872; C14orf156
Summary
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]
Expression
Ubiquitous expression in colon (RPKM 31.5), kidney (RPKM 28.3) and 25 other tissues See more
Orthologs

Genomic context

See SLIRP in Genome Data Viewer
Location:
14q24.3
Exon count:
5
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (77708071..77717598)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (78174414..78183941)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene alkB homolog 1, histone H2A dioxygenase Neighboring gene ribosomal protein L21 pseudogene 10 Neighboring gene zinc finger MYND-type containing 19 pseudogene 1 Neighboring gene SNW domain containing 1 Neighboring gene chromosome 14 open reading frame 178 Neighboring gene aarF domain containing kinase 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpu vpu HIV-1 Vpu is identified to have a physical interaction with SRA stem-loop interacting RNA binding protein (SLIRP) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
flagellated sperm motility IEA
Inferred from Electronic Annotation
more info
 
mitochondrion morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of mitochondrial RNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
single fertilization IEA
Inferred from Electronic Annotation
more info
 
spermatid development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
acrosomal vesicle IEA
Inferred from Electronic Annotation
more info
 
mitochondrion HDA PubMed 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sperm flagellum IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
SRA stem-loop-interacting RNA-binding protein, mitochondrial

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001267863.1NP_001254792.1  SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AY860853, BU944910, BU955571, BU960115
    Consensus CDS
    CCDS58331.1
    UniProtKB/Swiss-Prot
    Q9GZT3
    Related
    ENSP00000238688.5, ENST00000238688.9
    Conserved Domains (2) summary
    COG0724
    Location:2293
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12242
    Location:2090
    RRM_SLIRP; RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins
  2. NM_001267864.1NP_001254793.1  SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AY860853, BP289922, BU944910, BU960115
    Consensus CDS
    CCDS73668.1
    UniProtKB/Swiss-Prot
    Q9GZT3
    UniProtKB/TrEMBL
    A0A087WUN7
    Related
    ENSP00000478794.1, ENST00000613856.4
    Conserved Domains (2) summary
    COG0724
    Location:2284
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12242
    Location:2088
    RRM_SLIRP; RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins
  3. NM_031210.5NP_112487.1  SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_112487.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AY860853, BU944910, BU960115
    Consensus CDS
    CCDS9866.1
    UniProtKB/Swiss-Prot
    Q9GZT3
    Related
    ENSP00000450909.1, ENST00000557342.5
    Conserved Domains (1) summary
    cd12242
    Location:2092
    RRM_SLIRP; RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

RNA

  1. NR_052025.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AY860853, BM685909, BU944910, BU960115
    Related
    ENST00000555890.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    77708071..77717598
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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