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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
    NEW
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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)

    NEW Try the new Transcript table

    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.