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VNN2 vanin 2 [ Homo sapiens (human) ]

Gene ID: 8875, updated on 13-Mar-2020

Summary

Official Symbol
VNN2provided by HGNC
Official Full Name
vanin 2provided by HGNC
Primary source
HGNC:HGNC:12706
See related
Ensembl:ENSG00000112303 MIM:603571
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
FOAP-4; GPI-80
Summary
This gene product is a member of the Vanin family of proteins that share extensive sequence similarity with each other, and also with biotinidase. The family includes secreted and membrane-associated proteins, a few of which have been reported to participate in hematopoietic cell trafficking. No biotinidase activity has been demonstrated for any of the vanin proteins, however, they possess pantetheinase activity, which may play a role in oxidative-stress response. The encoded protein is a GPI-anchored cell surface molecule that plays a role in transendothelial migration of neutrophils. This gene lies in close proximity to, and in same transcriptional orientation as two other vanin genes on chromosome 6q23-q24. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, May 2011]
Expression
Biased expression in spleen (RPKM 12.9), lymph node (RPKM 11.0) and 11 other tissues See more
Orthologs

Genomic context

See VNN2 in Genome Data Viewer
Location:
6q23.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (132743503..132763489, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (133065009..133084598, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene vanin 1 Neighboring gene cyclin G1 pseudogene 1 Neighboring gene vanin 3 Neighboring gene RNA binding motif protein 11 pseudogene 1 Neighboring gene solute carrier family 18 member B1

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
pantetheine hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pantetheine hydrolase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
pantothenate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pantothenate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
pantothenate metabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
anchored component of membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
vascular non-inflammatory molecule 2
Names
Vannin 2
glycosylphosphatidyl inositol-anchored protein GPI-80
pantetheinase
NP_001229279.1
NP_004656.2
NP_511043.1
XP_006715656.1
XP_011534533.1
XP_016866897.1
XP_016866898.1

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.

Genomic

  1. NG_050645.1 RefSeqGene

    Range
    5001..24590
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001242350.2NP_001229279.1  vascular non-inflammatory molecule 2 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001229279.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two alternate in-frame exons in the coding region, compared to variant 1. The resulting protein (isoform 3) is shorter but has the same N- and C-termini compared to isoform 1.
    Source sequence(s)
    AB435064, BC064641, DC428640
    Consensus CDS
    CCDS56451.1
    UniProtKB/Swiss-Prot
    O95498
    Related
    ENSP00000436935.1, ENST00000525289.5
    Conserved Domains (1) summary
    cl11424
    Location:26180
    nitrilase; Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes
  2. NM_004665.5NP_004656.2  vascular non-inflammatory molecule 2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_004656.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB026705, BM153251, D89974, DC428640
    Consensus CDS
    CCDS5161.1
    UniProtKB/Swiss-Prot
    O95498
    Related
    ENSP00000322276.6, ENST00000326499.11
    Conserved Domains (1) summary
    cd07567
    Location:26329
    biotinidase_like; biotinidase and vanins (class 4 nitrilases)
  3. NM_078488.2NP_511043.1  vascular non-inflammatory molecule 2 isoform 2

    See identical proteins and their annotated locations for NP_511043.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream codon, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AK292125, BC064641, DC412933
    Consensus CDS
    CCDS5162.1
    UniProtKB/Swiss-Prot
    O95498
    Related
    ENSP00000436822.1, ENST00000525270.5
    Conserved Domains (1) summary
    cd07567
    Location:1276
    biotinidase_like; biotinidase and vanins (class 4 nitrilases)

RNA

  1. NR_034173.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate 5' 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)
    AB435062, BC064641, DC428640
  2. NR_034174.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate 5' exon and uses an alternate splice site, 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)
    AB435063, BC064641, DC428640
  3. NR_110143.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses an alternate internal splice site, 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)
    BC064641, BC144064, DC428640
    Related
    ENST00000392389.6
  4. NR_110144.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) uses an alternate internal splice site, 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)
    BC064641, BC126145, DC428640
    Related
    ENST00000418593.6
  5. NR_110145.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate 5' 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)
    AB026705, AK298719, BM153251, DC428640
  6. NR_110146.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks multiple consecutive exons, 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)
    AB435065, BC064641, DC428640

RefSeqs of Annotated Genomes: Homo sapiens Updated 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_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    132743503..132763489 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011408.1XP_016866897.1  vascular non-inflammatory molecule 2 isoform X3

  2. XM_017011409.1XP_016866898.1  vascular non-inflammatory molecule 2 isoform X3

  3. XM_006715593.3XP_006715656.1  vascular non-inflammatory molecule 2 isoform X1

    UniProtKB/Swiss-Prot
    O95498
    Conserved Domains (1) summary
    cd07567
    Location:1276
    biotinidase_like; biotinidase and vanins (class 4 nitrilases)
  4. XM_011536231.1XP_011534533.1  vascular non-inflammatory molecule 2 isoform X2

    Conserved Domains (1) summary
    cd07567
    Location:26329
    biotinidase_like; biotinidase and vanins (class 4 nitrilases)

RNA

  1. XR_002956311.1 RNA Sequence

    Related
    ENST00000422400.6
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