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

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: mouse all
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Genomic context

Location:: 14q24.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (77708071..77717598)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (71917426..71926933)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (78174414..78183941)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mitochondrial Protein SLIRP Affects Biosynthesis of Cytochrome c Oxidase Subunits in HEK293T Cells.
Title: Mitochondrial Protein SLIRP Affects Biosynthesis of Cytochrome c Oxidase Subunits in HEK293T Cells.
Pathogenic SLIRP variants as a novel cause of autosomal recessive mitochondrial encephalomyopathy with complex I and IV deficiency.
Title: Pathogenic SLIRP variants as a novel cause of autosomal recessive mitochondrial encephalomyopathy with complex I and IV deficiency.
Messenger RNA delivery to mitoribosomes - hints from a bacterial toxin.
Title: Messenger RNA delivery to mitoribosomes - hints from a bacterial toxin.
Effects of SLIRP on Sperm Motility and Oxidative Stress.
Title: Effects of SLIRP on Sperm Motility and Oxidative Stress.
Interaction between androgen receptor and coregulator SLIRP is regulated by Ack1 tyrosine kinase and androgen.
Title: Interaction between androgen receptor and coregulator SLIRP is regulated by Ack1 tyrosine kinase and androgen.
Study demonstrated that the LRPPRC-SLIRP complex is a global RNA chaperone that stabilizes RNA structures to expose the required sites for translation, stabilization, and polyadenylation.
Title: LRPPRC-mediated folding of the mitochondrial transcriptome.
assessed, by using CRISPR-Cas9-introduced affinity tag and ChIP-Seq analysis, the genome-wide occupancy of SLIRP, and showed that the protein binds preferentially to G-rich DNA sequences that can fold into G4 structures
Title: Identification of SLIRP as a G Quadruplex-Binding Protein.
LRPPRC displays a broad and strong RNA binding capacity in vitro in contrast to SLIRP that associates only weakly with RNA.
Title: SLIRP stabilizes LRPPRC via an RRM-PPR protein interface.
Although SLIRP is not involved in mediating bcl-2 ability to protect from apoptosis and oxidative damage, bcl-2 binds and stabilizes SLIRP protein and regulates mitochondrial mRNA levels. The BH4 domain of bcl-2 has a role in maintaining this binding.
Title: Affinity purification-mass spectrometry analysis of bcl-2 interactome identified SLIRP as a novel interacting protein.
The LRPPRC/SLIRP complex suppressed 3' exonucleolytic mRNA degradation mediated by PNPase and SUV3.
Title: LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G36014 (e-PCR)
- UniSTS:43996

D14S857 (e-PCR)
- UniSTS:16865

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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	TAS Traceable Author Statement more info
located_in mitochondrion	HDA more info	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

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

NCBI Reference Sequences (RefSeq)

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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)

NM_001267863.1 → NP_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:22 → 93

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12242
Location:20 → 90

RRM_SLIRP; RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins
NM_001267864.1 → NP_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:22 → 84

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12242
Location:20 → 88

RRM_SLIRP; RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins
NM_031210.6 → NP_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:20 → 92

RRM_SLIRP; RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

RNA

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