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

    Gene ID: 81892, updated on 9-Dec-2024

    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; AllianceGenome:HGNC:20495
    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
    NEW
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    Try the new Transcript table

    Genomic context

    See SLIRP in Genome Data Viewer
    Location:
    14q24.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77708071..77717598)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71917426..71926933)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (78174414..78183941)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:78151521-78152022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:78152023-78152522 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 ATAC-STARR-seq lymphoblastoid active region 8810 Neighboring gene SNW domain containing 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78226689-78227463 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:78228238-78229012 Neighboring gene SLIRP overlapping transcript 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78257054-78257970 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5980 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78265777-78266315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:78266316-78266854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8813 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78268449-78269288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8814 Neighboring gene aarF domain containing kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:78379195-78379710

    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 Functions

    What'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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in flagellated sperm motility IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitochondrion organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of mitochondrial RNA catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in single fertilization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in acrosomal vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
     
    located_in mitochondrion HDA PubMed 
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
     
    located_in 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)

    NEW Try the new Transcript table

    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/TrEMBL
      G3V4X6
      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/TrEMBL
      A0A087WUN7, G3V4X6
      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_031210.6NP_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, BU960115
      Consensus CDS
      CCDS9866.1
      UniProtKB/Swiss-Prot
      J3KMY7, Q9GZT3
      UniProtKB/TrEMBL
      H0YJ40
      Related
      ENSP00000450909.1, ENST00000557342.6
      Conserved Domains (1) summary
      cd12242
      Location:2092
      RRM_SLIRP; RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

    RNA

    1. NR_052025.2 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, BU960115
      Related
      ENST00000555890.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      71917426..71926933
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)