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VSTM1 V-set and transmembrane domain containing 1 [ Homo sapiens (human) ]

Gene ID: 284415, updated on 13-May-2022

Summary

Official Symbol
VSTM1provided by HGNC
Official Full Name
V-set and transmembrane domain containing 1provided by HGNC
Primary source
HGNC:HGNC:29455
See related
Ensembl:ENSG00000189068 MIM:616804; AllianceGenome:HGNC:29455
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
SIRL1; SIRL-1; UNQ3033
Summary
Predicted to enable cytokine activity. Predicted to be involved in immune system process and signal transduction. Predicted to be located in extracellular space. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward bone marrow (RPKM 28.7) See more
Orthologs
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Try the new Transcript table

Genomic context

See VSTM1 in Genome Data Viewer
Location:
19q13.42
Exon count:
13
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54040825..54063897, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57119327..57142392, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54544079..54567151, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene calcium voltage-gated channel auxiliary subunit gamma 6 Neighboring gene Sharpr-MPRA regulatory region 12456 Neighboring gene T cell-interacting, activating receptor on myeloid cells 1 Neighboring gene osteoclast associated Ig-like receptor

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC119160, MGC119161

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytokine activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in immune system process IEA
Inferred from Electronic Annotation
more info
 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in extracellular space IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
V-set and transmembrane domain-containing protein 1
Names
LAIR homolog
OSCAR-like transcript-1
signal inhibitory receptor on leukocytes-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_001288791.2NP_001275720.1  V-set and transmembrane domain-containing protein 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks one exon and contains an alternate exon in the 5' coding region, which results in a frameshift and use of an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC012314, AI457604, AY358542, FJ584317, FJ584320
    UniProtKB/Swiss-Prot
    Q6UX27
    UniProtKB/TrEMBL
    D2DJS6
  2. NM_001288792.2NP_001275721.1  V-set and transmembrane domain-containing protein 1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001275721.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
    Source sequence(s)
    AI457604, AY358542, BC100943, FJ584317
    Consensus CDS
    CCDS74442.1
    UniProtKB/Swiss-Prot
    Q6UX27
    Related
    ENSP00000365813.1, ENST00000376626.5
    Conserved Domains (2) summary
    smart00410
    Location:35117
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  3. NM_001288793.2NP_001275722.1  V-set and transmembrane domain-containing protein 1 isoform 4

    See identical proteins and their annotated locations for NP_001275722.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks three consecutive exons in the central coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter, compared to isoform 1.
    Source sequence(s)
    AI457604, AY358542, FJ584319
    Consensus CDS
    CCDS74441.1
    UniProtKB/Swiss-Prot
    Q6UX27
    UniProtKB/TrEMBL
    D2DJS5
    Related
    ENSP00000444153.2, ENST00000366170.6
  4. NM_198481.4NP_940883.2  V-set and transmembrane domain-containing protein 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_940883.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AI457604, AY358542, BG189223
    Consensus CDS
    CCDS12872.1
    UniProtKB/Swiss-Prot
    Q6UX27
    Related
    ENSP00000343366.2, ENST00000338372.7
    Conserved Domains (2) summary
    smart00410
    Location:35117
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain

RNA

  1. NR_110142.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC012314, AI457604, AY358542, FJ882051

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    54040825..54063897 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526849.2XP_011525151.1  V-set and transmembrane domain-containing protein 1 isoform X6

    See identical proteins and their annotated locations for XP_011525151.1

    Conserved Domains (2) summary
    smart00410
    Location:35117
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  2. XM_011526848.2XP_011525150.1  V-set and transmembrane domain-containing protein 1 isoform X4

    See identical proteins and their annotated locations for XP_011525150.1

    Conserved Domains (2) summary
    smart00410
    Location:35117
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  3. XM_011526846.2XP_011525148.1  V-set and transmembrane domain-containing protein 1 isoform X2

    See identical proteins and their annotated locations for XP_011525148.1

    Conserved Domains (2) summary
    smart00410
    Location:35117
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  4. XM_011526847.2XP_011525149.1  V-set and transmembrane domain-containing protein 1 isoform X3

    See identical proteins and their annotated locations for XP_011525149.1

    Conserved Domains (2) summary
    smart00410
    Location:35117
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  5. XM_011526845.2XP_011525147.1  V-set and transmembrane domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011525147.1

    Conserved Domains (2) summary
    smart00410
    Location:35117
    IG_like; Immunoglobulin like
    cl11960
    Location:27118
    Ig; Immunoglobulin domain
  6. XM_047438667.1XP_047294623.1  V-set and transmembrane domain-containing protein 1 isoform X5

    Related
    ENSP00000495014.1, ENST00000645936.1
  7. XM_017026666.2XP_016882155.1  V-set and transmembrane domain-containing protein 1 isoform X7

    UniProtKB/Swiss-Prot
    Q6UX27
    Related
    ENSP00000401926.1, ENST00000447872.5
    Conserved Domains (1) summary
    cl11960
    Location:27118
    Ig; Immunoglobulin domain

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NW_003571056.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NW_003571057.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NW_003571058.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NW_003571059.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p14 ALT_REF_LOCI_8

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

    Range
    15192..38264 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    57119327..57142392 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)