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SRP54 signal recognition particle 54 [ Homo sapiens (human) ]

Gene ID: 6729, updated on 1-Jun-2020

Summary

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Official Symbol
SRP54provided by HGNC
Official Full Name
signal recognition particle 54provided by HGNC
Primary source
HGNC:HGNC:11301
See related
Ensembl:ENSG00000100883 MIM:604857
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
SCN8
Expression
Ubiquitous expression in testis (RPKM 26.2), thyroid (RPKM 18.4) and 25 other tissues See more
Orthologs
mouse all

Genomic context

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See SRP54 in Genome Data Viewer
Location:
14q13.2
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (34982898..35029567)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (35451901..35498773)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene bromodomain adjacent to zinc finger domain 1A Neighboring gene uncharacterized LOC112268124 Neighboring gene SRP54 antisense RNA 1 (head to head) Neighboring gene immunoglobulin (CD79A) binding protein 1 pseudogene 1 Neighboring gene family with sequence similarity 177 member A1 Neighboring gene uncharacterized LOC101927178 Neighboring gene protein phosphatase 2 regulatory subunit B''gamma Neighboring gene protein only RNase P catalytic subunit

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Mutations in the SRP54 gene cause severe congenital neutropenia as well as Shwachman-Diamond-like syndrome. Bellanné-Chantelot C, et al. Blood, 2018 Sep 20. PMID 29914977, Free PMC Article
  2. Assembly of the human signal recognition particle (SRP): overlap of regions required for binding of protein SRP54 and assembly control. Yin J, et al. RNA, 2001 Oct. PMID 11680843, Free PMC Article
  3. Crystal structure of the conserved subdomain of human protein SRP54M at 2.1 A resolution: evidence for the mechanism of signal peptide binding. Clemons WM Jr, et al. J Mol Biol, 1999 Sep 24. PMID 10497032
  4. Sequence of the highly conserved gene encoding the human 54kDa subunit of signal recognition particle. Patel S, et al. DNA Seq, 1996. PMID 8722571
  5. Binding site of the M-domain of human protein SRP54 determined by systematic site-directed mutagenesis of signal recognition particle RNA. Gowda K, et al. Nucleic Acids Res, 1997 Jan 15. PMID 9016569, Free PMC Article

See all (53) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Whole exome sequencing discloses heterozygous variants in the DNAJC21 and EFL1 genes but not in SRP54 in 6 out of 16 patients with Shwachman-Diamond Syndrome carrying biallelic SBDS mutations.
    Title: Whole exome sequencing discloses heterozygous variants in the DNAJC21 and EFL1 genes but not in SRP54 in 6 out of 16 patients with Shwachman-Diamond Syndrome carrying biallelic SBDS mutations.
  2. e show that SRP RNA does not bind to the ribosome, while SRP binds with nanomolar affinity involving a two-step mechanism of the key-player SRP54. Ultrasensitive binding of SRP68/72 indicates avidity by multiple binding sites that are dominated by the C-terminus of SRP72
    Title: Reconstitution of the human SRP system and quantitative and systematic analysis of its ribosome interactions.
  3. This study identified SRP54 mutations in congenital neutropenia. SRP54 mutations induce endoplasmic reticulum stress and autophagy associated with apoptosis.
    Title: Mutations in the <i>SRP54</i> gene cause severe congenital neutropenia as well as Shwachman-Diamond-like syndrome.
  4. autosomal dominant mutations in SRP54, a key member of the cotranslation protein-targeting pathway, lead to syndromic neutropenia with a Shwachman-Diamond-like phenotype.
    Title: Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features.
  5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  6. crystal structure of a human SRP ternary complex consisting of SRP19, the M domain of SRP54 and the S domain of 7SL RNA
    Title: Induced structural changes of 7SL RNA during the assembly of human signal recognition particle.
Submit: New GeneRIF Correction

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

Associated conditions

Description Tests
NEUTROPENIA, SEVERE CONGENITAL, 8, AUTOSOMAL DOMINANT
MedGen: CN263232 OMIM: 618752 GeneReviews: Not available
not available
Shwachman syndrome
MedGen: C0272170 GeneReviews: Shwachman-Diamond Syndrome
Compare labs
Shwachman-Diamond syndrome 1
MedGen: C4692625 OMIM: 260400 GeneReviews: Shwachman-Diamond Syndrome, Pancreatitis Overview
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, signal recognition particle 54kDa (SRP54), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
7S RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
7S RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
GDP binding IDA
Inferred from Direct Assay
more info
 PubMed 
GTP binding IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
contributes_to GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
RNA binding HDA PubMed 
drug binding IDA
Inferred from Direct Assay
more info
 PubMed 
endoplasmic reticulum signal peptide binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
endoplasmic reticulum signal peptide binding IDA
Inferred from Direct Assay
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
ribonucleoprotein complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
SRP-dependent cotranslational protein targeting to membrane IC
Inferred by Curator
more info
 PubMed 
SRP-dependent cotranslational protein targeting to membrane TAS
Traceable Author Statement
more info
  
SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition ISS
Inferred from Sequence or Structural Similarity
more info
  
SRP-dependent cotranslational protein targeting to membrane, translocation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
SRP-dependent cotranslational protein targeting to membrane, translocation ISS
Inferred from Sequence or Structural Similarity
more info
  
protein targeting to ER IMP
Inferred from Mutant Phenotype
more info
 PubMed 
response to drug IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
cytosol IDA
Inferred from Direct Assay
more info
  
cytosol TAS
Traceable Author Statement
more info
  
nuclear speck IEA
Inferred from Electronic Annotation
more info
  
NOT nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
signal recognition particle, endoplasmic reticulum targeting IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
signal recognition particle, endoplasmic reticulum targeting IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
signal recognition particle 54 kDa protein
Names
signal recognition particle 54kD
signal recognition particle 54kDa

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)

  1. NM_001146282.1 → NP_001139754.1  signal recognition particle 54 kDa protein isoform 2

    See identical proteins and their annotated locations for NP_001139754.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks a portion of the 5' coding region and uses a distinct translational start codon, compared to variant 1. The resulting isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK300824, BC000652, DA495064
    Consensus CDS
    CCDS53893.1
    UniProtKB/Swiss-Prot
    P61011
    Related
    ENSP00000440629.1, ENST00000546080.5
    Conserved Domains (1) summary
    TIGR01425
    Location:8 → 381
    SRP54_euk; signal recognition particle protein SRP54

  2. NM_003136.4 → NP_003127.1  signal recognition particle 54 kDa protein isoform 1

    See identical proteins and their annotated locations for NP_003127.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC000652, DA495064
    Consensus CDS
    CCDS9652.1
    UniProtKB/Swiss-Prot
    P61011
    Related
    ENSP00000216774.6, ENST00000216774.11
    Conserved Domains (1) summary
    TIGR01425
    Location:2 → 430
    SRP54_euk; signal recognition particle protein SRP54

RefSeqs of Annotated Genomes: Homo sapiens Updated 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
    34982898..35029567
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005268024.3 → XP_005268081.1  signal recognition particle 54 kDa protein isoform X2

    Conserved Domains (1) summary
    cl27330
    Location:2 → 385
    FlhF; Flagellar biosynthesis GTPase FlhF [Cell motility]

  2. XM_017021615.2 → XP_016877104.1  signal recognition particle 54 kDa protein isoform X3

    Conserved Domains (2) summary
    pfam00448
    Location:1 → 190
    SRP54; SRP54-type protein, GTPase domain
    pfam02978
    Location:222 → 325
    SRP_SPB; Signal peptide binding domain

  3. XM_011537106.1 → XP_011535408.1  signal recognition particle 54 kDa protein isoform X1

    See identical proteins and their annotated locations for XP_011535408.1

    UniProtKB/Swiss-Prot
    P61011
    Conserved Domains (1) summary
    TIGR01425
    Location:2 → 430
    SRP54_euk; signal recognition particle protein SRP54
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P61011.1 GenPept UniProtKB/Swiss-Prot:P61011

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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