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

    Gene ID: 6729, updated on 27-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
    all
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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
    • 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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    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
    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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