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

Summary

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: all
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Genomic context

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_000014.9 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 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?

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.
Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia.
Title: Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia.
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.
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.
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.
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.
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.
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.
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.
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.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neutropenia, severe congenital, 8, autosomal dominant MedGen: C5203411 OMIM: 618752 GeneReviews: Not available	not available
Shwachman syndrome MedGen: C0272170 GeneReviews: Shwachman-Diamond Syndrome	not available
Shwachman-Diamond syndrome 1 MedGen: C4692625 OMIM: 260400 GeneReviews: Shwachman-Diamond Syndrome, Pancreatitis Overview	not available

Variation

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See Variation Viewer (GRCh37.p13)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G35379 (e-PCR)
- UniSTS:19713

RH70669 (e-PCR)
- UniSTS:41140

RH68420 (e-PCR)
- UniSTS:62429

G35634 (e-PCR)
- UniSTS:76017

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 more info	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

EC 3.6.5.4

NP_001397946.1

EC 3.6.5.4

NP_003127.1

EC 3.6.5.4

XP_011535408.1

EC 3.6.5.4

XP_047287683.1

EC 3.6.5.4

XP_054232621.1

EC 3.6.5.4

XP_054232622.1

EC 3.6.5.4

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_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
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
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

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

34982992..35029567

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

29181721..29228319

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B2R759, B4DUW6, P13624, P61011
XM_054376647.1 → XP_054232622.1 signal recognition particle subunit SRP54 isoform X2