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VAT1L vesicle amine transport 1 like [ Homo sapiens (human) ]

Gene ID: 57687, updated on 5-Mar-2024

Summary

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Official Symbol
VAT1Lprovided by HGNC
Official Full Name
vesicle amine transport 1 likeprovided by HGNC
Primary source
HGNC:HGNC:29315
See related
Ensembl:ENSG00000171724 MIM:620202; AllianceGenome:HGNC:29315
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
Summary
Predicted to enable oxidoreductase activity and zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in adrenal (RPKM 44.1), brain (RPKM 16.6) and 3 other tissues See more
Orthologs
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Genomic context

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See VAT1L in Genome Data Viewer
Location:
16q23.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (77788564..77980107)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (83844682..84036081)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (77822461..78014004)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2131 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45434 Neighboring gene Sharpr-MPRA regulatory region 41 Neighboring gene uncharacterized LOC107984878 Neighboring gene nudix hydrolase 7 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:77866929-77867894 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:77867895-77868858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:77885719-77886220 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:77911218-77912417 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:77928177-77928677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:77952963-77953462 Neighboring gene peptidylprolyl isomerase A pseudogene 50 Neighboring gene uncharacterized LOC105371351 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11154 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78000722-78001339 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78001340-78001958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:78003196-78003813 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45488 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:78025071-78026270 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78026297-78026990 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78026991-78027683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:78028377-78029069 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:78029289-78030488 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45524 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7735 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45548 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45593 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45596 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45605 Neighboring gene C-type lectin domain family 3 member A Neighboring gene keratin 8 pseudogene 22

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. Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects. Dastani Z, et al. Eur J Hum Genet, 2010 Mar. PMID 19844255, Free PMC Article
  2. Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. Sherva R, et al. Alzheimers Dement, 2014 Jan. PMID 23535033, Free PMC Article
  3. A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. Wang KS, et al. Schizophr Res, 2010 Dec. PMID 20889312
  4. Interaction between the scaffold proteins CBP by IQGAP1 provides an interface between gene expression and cytoskeletal activity. Kosol S, et al. Sci Rep, 2020 Apr 1. PMID 32238831, Free PMC Article
  5. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Aug 31. PMID 10997877

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
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

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
EBI GWAS Catalog
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1576

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
synaptic vesicle membrane protein VAT-1 homolog-like
Names
vesicle amine transport protein 1 homolog (T. californica)-like
vesicle amine transport protein 1 homolog-like (T. californica)

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_020927.3 → NP_065978.1  synaptic vesicle membrane protein VAT-1 homolog-like

    See identical proteins and their annotated locations for NP_065978.1

    Status: VALIDATED

    Source sequence(s)
    AA609348, AC010650, AK290153, BC033537, HY132852
    Consensus CDS
    CCDS32492.1
    UniProtKB/Swiss-Prot
    Q8IYW8, Q9HCJ6
    UniProtKB/TrEMBL
    A8K288
    Related
    ENSP00000303129.2, ENST00000302536.3
    Conserved Domains (1) summary
    cd08275
    Location:43 → 380
    MDR3; Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    77788564..77980107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    83844682..84036081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HCJ6.2 GenPept UniProtKB/Swiss-Prot:Q9HCJ6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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