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

Gene ID: 6729, updated on 3-Nov-2024

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; AllianceGenome:HGNC:11301
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
Summary
Enables several functions, including 7S RNA binding activity; endoplasmic reticulum signal peptide binding activity; and guanyl ribonucleotide binding activity. Contributes to GTPase activity. Involved in granulocyte differentiation and protein targeting to ER. Located in cytosol and nucleus. Part of signal recognition particle, endoplasmic reticulum targeting. Implicated in severe congenital neutropenia 8. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 26.2), thyroid (RPKM 18.4) and 25 other tissues See more
Orthologs
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Genomic context

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See SRP54 in Genome Data Viewer
Location:
14q13.2
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (34982992..35029567)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (29181721..29228319)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (35452198..35498773)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene bromodomain adjacent to zinc finger domain 1A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5671 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5672 Neighboring gene BAZ1A antisense RNA 1 Neighboring gene SRP54 antisense RNA 1 Neighboring gene IGBP1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 9881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8256 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:35451517-35452218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8262 Neighboring gene family with sequence similarity 177 member A1 Neighboring gene uncharacterized LOC101927178 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:35571935-35572102 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:35581755-35582536 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:35590400-35591599 Neighboring gene protein phosphatase 2 regulatory subunit B''gamma Neighboring gene PRORP-PSMA6 readthrough 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 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. Sequence of the highly conserved gene encoding the human 54kDa subunit of signal recognition particle. Patel S, et al. DNA Seq, 1996. PMID 8722571
  2. Congenital neutropenia with variable clinical presentation in novel mutation of the SRP54 gene. Goldberg L, et al. Pediatr Blood Cancer, 2020 Jun. PMID 32277798
  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. 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
  5. 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

See all (105) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Autosomal dominant Shwachman-Diamond syndrome with a novel heterozygous missense variant in the SRP54 gene causing severe phenotypic features.
    Title: Autosomal dominant Shwachman-Diamond syndrome with a novel heterozygous missense variant in the SRP54 gene causing severe phenotypic features.
  2. Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia.
    Title: Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia.
  3. SRP54 mutations induce congenital neutropenia via dominant-negative effects on XBP1 splicing.
    Title: SRP54 mutations induce congenital neutropenia via dominant-negative effects on XBP1 splicing.
  4. Congenital neutropenia with variable clinical presentation in novel mutation of the SRP54 gene.
    Title: Congenital neutropenia with variable clinical presentation in novel mutation of the SRP54 gene.
  5. 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.
  6. 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.
  7. This study identified SRP54 mutations in congenital neutropenia. SRP54 mutations induce endoplasmic reticulum stress and autophagy associated with apoptosis.
    Title: Mutations in the SRP54 gene cause severe congenital neutropenia as well as Shwachman-Diamond-like syndrome.
  8. 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.
  9. 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.
  10. 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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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
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
enables 7S RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 7S RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables GDP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTP binding IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTPase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables RNA binding HDA PubMed 
enables endoplasmic reticulum signal peptide binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables endoplasmic reticulum signal peptide binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribonucleoprotein complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within SRP-dependent cotranslational protein targeting to membrane IC
Inferred by Curator
more info
 PubMed 
involved_in SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in SRP-dependent cotranslational protein targeting to membrane, translocation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in SRP-dependent cotranslational protein targeting to membrane, translocation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in exocrine pancreas development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in granulocyte differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neutrophil chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein targeting to ER IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
NOT located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of signal recognition particle, endoplasmic reticulum targeting IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of 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 subunit SRP54
Names
signal recognition particle 54 kDa protein
signal recognition particle 54kD
signal recognition particle 54kDa
NP_001139754.1
NP_001397946.1
NP_003127.1
XP_011535408.1
XP_047287683.1
XP_054232621.1
XP_054232622.1

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_001146282.2 → NP_001139754.1  signal recognition particle subunit SRP54 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
    UniProtKB/TrEMBL
    G3V4F7
    Related
    ENSP00000451775.1, ENST00000555557.5
    Conserved Domains (1) summary
    TIGR01425
    Location:8 → 381
    SRP54_euk; signal recognition particle protein SRP54

  2. NM_001411017.1 → NP_001397946.1  signal recognition particle subunit SRP54 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL049776
    Consensus CDS
    CCDS91863.1
    UniProtKB/TrEMBL
    G3V480
    Related
    ENSP00000451647.2, ENST00000555746.6

  3. NM_003136.4 → NP_003127.1  signal recognition particle subunit SRP54 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
    B2R759, B4DUW6, P13624, P61011
    UniProtKB/TrEMBL
    A0A7I2V5K0
    Related
    ENSP00000216774.6, ENST00000216774.11
    Conserved Domains (1) summary
    TIGR01425
    Location:2 → 430
    SRP54_euk; signal recognition particle protein SRP54

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
    34982992..35029567
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537106.1 → XP_011535408.1  signal recognition particle subunit SRP54 isoform X1

    See identical proteins and their annotated locations for XP_011535408.1

    UniProtKB/Swiss-Prot
    B2R759, B4DUW6, P13624, P61011
    UniProtKB/TrEMBL
    A0A7I2V5K0
    Related
    ENSP00000504673.1, ENST00000677647.1
    Conserved Domains (1) summary
    TIGR01425
    Location:2 → 430
    SRP54_euk; signal recognition particle protein SRP54

  2. XM_047431727.1 → XP_047287683.1  signal recognition particle subunit SRP54 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    29181721..29228319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376646.1 → XP_054232621.1  signal recognition particle subunit SRP54 isoform X1

    UniProtKB/Swiss-Prot
    B2R759, B4DUW6, P13624, P61011

  2. XM_054376647.1 → XP_054232622.1  signal recognition particle subunit SRP54 isoform X2

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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