Format

Send to:

Choose Destination

SCAMP1 secretory carrier membrane protein 1 [ Homo sapiens (human) ]

Gene ID: 9522, updated on 17-Jun-2019

Summary

Official Symbol
SCAMP1provided by HGNC
Official Full Name
secretory carrier membrane protein 1provided by HGNC
Primary source
HGNC:HGNC:10563
See related
Ensembl:ENSG00000085365 MIM:606911
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SCAMP; SCAMP37
Summary
This gene product belongs to the SCAMP family of proteins, which are secretory carrier membrane proteins. They function as carriers to the cell surface in post-golgi recycling pathways. Different family members are highly related products of distinct genes, and are usually expressed together. These findings suggest that these protein family members may function at the same site during vesicular transport rather than in separate pathways. A pseudogene of this gene has been defined on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
Expression
Ubiquitous expression in brain (RPKM 21.2), thyroid (RPKM 14.8) and 25 other tissues See more
Orthologs

Genomic context

See SCAMP1 in Genome Data Viewer
Location:
5q14.1
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (78360503..78480739)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (77656339..77776562)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NFE2L2 motif-containing MPRA enhancer 287 Neighboring gene RNA, U6 small nuclear 183, pseudogene Neighboring gene SCAMP1 antisense RNA 1 Neighboring gene LHFPL tetraspan subfamily member 2 Neighboring gene Sharpr-MPRA regulatory region 10457 Neighboring gene high mobility group box 1 pseudogene 21

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease.
NHGRI GWA Catalog

Pathways from BioSystems

  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
neutrophil degranulation TAS
Traceable Author Statement
more info
 
post-Golgi vesicle-mediated transport TAS
Traceable Author Statement
more info
PubMed 
protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
clathrin-coated vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
recycling endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
recycling endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
specific granule membrane TAS
Traceable Author Statement
more info
 
synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zymogen granule membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
secretory carrier-associated membrane protein 1

NCBI Reference Sequences (RefSeq)

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_001290229.2NP_001277158.1  secretory carrier-associated membrane protein 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
    Source sequence(s)
    AK001417, AK304452, AL049223, AW590077, BC034048, CR542286
    Consensus CDS
    CCDS78025.1
    UniProtKB/Swiss-Prot
    O15126
    UniProtKB/TrEMBL
    A0A087WXB0, B4E2V7
    Related
    ENSP00000480865.1, ENST00000618166.4
    Conserved Domains (2) summary
    pfam04144
    Location:91266
    SCAMP; SCAMP family
    cl03075
    Location:3989
    GrpE; nucleotide exchange factor GrpE
  2. NM_004866.6NP_004857.4  secretory carrier-associated membrane protein 1 isoform 1

    See identical proteins and their annotated locations for NP_004857.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK001417, AL049223, AW590077, BC034048, CR542286, DB213762
    Consensus CDS
    CCDS75264.1
    UniProtKB/Swiss-Prot
    O15126
    Related
    ENSP00000481022.1, ENST00000621999.5
    Conserved Domains (1) summary
    pfam04144
    Location:117292
    SCAMP; SCAMP family

RNA

  1. NR_110885.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK001417, AL049223, AW590077, BC009787, BC034048, DB213762

RefSeqs of Annotated Genomes: Homo sapiens 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_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    78360503..78480739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543727.3XP_011542029.1  secretory carrier-associated membrane protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011542029.1

    Conserved Domains (2) summary
    pfam04144
    Location:117258
    SCAMP; SCAMP family
    cl03075
    Location:65115
    GrpE; nucleotide exchange factor GrpE

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_052822.2: Suppressed sequence

    Description
    NM_052822.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Support Center