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

Gene ID: 9522, updated on 17-Jun-2024

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; AllianceGenome:HGNC:10563
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
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Genomic context

See SCAMP1 in Genome Data Viewer
Location:
5q14.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (78360617..78480739)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (78842266..78962217)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (77656441..77776562)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901010 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77655493-77656089 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77656090-77656686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16120 Neighboring gene SCAMP1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:77687375-77687953 Neighboring gene MPRA-validated peak5302 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77753154-77753763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77788199-77788702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22709 Neighboring gene Sharpr-MPRA regulatory region 4849 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77800693-77801201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77805941-77806562 Neighboring gene LHFPL tetraspan subfamily member 2 Neighboring gene Sharpr-MPRA regulatory region 4833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77828783-77829282 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77838469-77839288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77839289-77840106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22713 Neighboring gene Sharpr-MPRA regulatory region 10457 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:77911679-77912878 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:77922186-77922385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77928669-77929170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77929171-77929670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16123 Neighboring gene uncharacterized LOC124900191 Neighboring gene high mobility group box 1 pseudogene 21 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:77995230-77996429 Neighboring gene Sharpr-MPRA regulatory region 2428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22719

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 Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in endocytosis IEA
Inferred from Electronic Annotation
more info
 
involved_in establishment of localization in cell IEA
Inferred from Electronic Annotation
more info
 
involved_in exocytosis IEA
Inferred from Electronic Annotation
more info
 
involved_in post-Golgi vesicle-mediated transport TAS
Traceable Author Statement
more info
PubMed 
involved_in protein transport IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in clathrin-coated vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
is_active_in recycling endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in recycling endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in specific granule membrane TAS
Traceable Author Statement
more info
 
located_in synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in trans-Golgi network membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in 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)

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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_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/TrEMBL
    A0A087WXB0, B4E2V7
    Related
    ENSP00000480865.1, ENST00000618166.4
    Conserved Domains (1) summary
    pfam04144
    Location:91266
    SCAMP; SCAMP family
  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, O43587, Q6FG23, Q96BX1, Q96QK5
    UniProtKB/TrEMBL
    A8K2G0
    Related
    ENSP00000481022.1, ENST00000621999.5
    Conserved Domains (1) summary
    pfam04144
    Location:117292
    SCAMP; SCAMP family

RNA

  1. NR_110885.2 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    78360617..78480739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543727.4XP_011542029.1  secretory carrier-associated membrane protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011542029.1

    UniProtKB/TrEMBL
    A8K2G0
    Conserved Domains (2) summary
    pfam04144
    Location:117258
    SCAMP; SCAMP family
    cl03075
    Location:65115
    GrpE; nucleotide exchange factor GrpE

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    78842266..78962217
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353828.1XP_054209803.1  secretory carrier-associated membrane protein 1 isoform X1

    UniProtKB/TrEMBL
    A8K2G0

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.