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VIPAS39 VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog [ Homo sapiens (human) ]

Gene ID: 63894, updated on 24-Nov-2020

Summary

Official Symbol
VIPAS39provided by HGNC
Official Full Name
VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homologprovided by HGNC
Primary source
HGNC:HGNC:20347
See related
Ensembl:ENSG00000151445 MIM:613401
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
SPE39; VIPAR; SPE-39; VPS16B; hSPE-39; C14orf133
Summary
This gene encodes a protein involved in the sorting of lysosomal proteins. Mutations in this gene are associated with ARCS2 (arthrogryposis, renal dysfunction, and cholestasis-2). Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jul 2010]
Expression
Ubiquitous expression in testis (RPKM 8.8), ovary (RPKM 6.7) and 25 other tissues See more
Orthologs

Genomic context

See VIPAS39 in Genome Data Viewer
Location:
14q24.3
Exon count:
22
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (77426675..77457727, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (77893018..77923983, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene sterile alpha motif domain containing 15 Neighboring gene HNF1 motif-containing MPRA enhancer 277 Neighboring gene NADP dependent oxidoreductase domain containing 1 Neighboring gene activator of HSP90 ATPase activity 1 Neighboring gene isthmin 2

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

  • FLJ12707

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
NOT autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
collagen fibril organization IEA
Inferred from Electronic Annotation
more info
 
collagen metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosome to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT endosome to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular protein transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
peptidyl-lysine hydroxylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
post-translational protein modification IEA
Inferred from Electronic Annotation
more info
 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
vacuolar transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
NOT HOPS complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
spermatogenesis-defective protein 39 homolog
Names
VPS33B-interacting protein involved in polarity and apical protein restriction

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_023421.1 RefSeqGene

    Range
    5001..35966
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001193314.2NP_001180243.1  spermatogenesis-defective protein 39 homolog isoform 1

    See identical proteins and their annotated locations for NP_001180243.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).
    Source sequence(s)
    AF111168
    Consensus CDS
    CCDS9862.1
    UniProtKB/Swiss-Prot
    Q9H9C1
    UniProtKB/TrEMBL
    Q6IA61
    Related
    ENSP00000452181.1, ENST00000553888.5
    Conserved Domains (1) summary
    pfam09787
    Location:26471
    Golgin_A5; Golgin subfamily A member 5
  2. NM_001193315.2NP_001180244.1  spermatogenesis-defective protein 39 homolog isoform 1

    See identical proteins and their annotated locations for NP_001180244.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).
    Source sequence(s)
    AF111168, AK022769, AW629161
    Consensus CDS
    CCDS9862.1
    UniProtKB/Swiss-Prot
    Q9H9C1
    UniProtKB/TrEMBL
    Q6IA61
    Related
    ENSP00000452191.1, ENST00000557658.6
    Conserved Domains (1) summary
    pfam09787
    Location:26471
    Golgin_A5; Golgin subfamily A member 5
  3. NM_001193316.2NP_001180245.1  spermatogenesis-defective protein 39 homolog isoform 2

    See identical proteins and their annotated locations for NP_001180245.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
    Source sequence(s)
    AF111168
    Consensus CDS
    CCDS53905.1
    UniProtKB/Swiss-Prot
    Q9H9C1
    Related
    ENSP00000404815.2, ENST00000448935.6
    Conserved Domains (1) summary
    pfam09787
    Location:26422
    Golgin_A5; Golgin subfamily A member 5
  4. NM_001193317.2NP_001180246.1  spermatogenesis-defective protein 39 homolog isoform 1

    See identical proteins and their annotated locations for NP_001180246.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).
    Source sequence(s)
    AF111168
    Consensus CDS
    CCDS9862.1
    UniProtKB/Swiss-Prot
    Q9H9C1
    UniProtKB/TrEMBL
    B4DMB7, Q6IA61
    Related
    ENSP00000451857.1, ENST00000556412.4
    Conserved Domains (1) summary
    pfam09787
    Location:26471
    Golgin_A5; Golgin subfamily A member 5
  5. NM_022067.4NP_071350.2  spermatogenesis-defective protein 39 homolog isoform 1

    See identical proteins and their annotated locations for NP_071350.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).
    Source sequence(s)
    AF111168
    Consensus CDS
    CCDS9862.1
    UniProtKB/Swiss-Prot
    Q9H9C1
    UniProtKB/TrEMBL
    Q6IA61
    Related
    ENSP00000339122.2, ENST00000343765.6
    Conserved Domains (1) summary
    pfam09787
    Location:26471
    Golgin_A5; Golgin subfamily A member 5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    77426675..77457727 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024449688.1XP_024305456.1  spermatogenesis-defective protein 39 homolog isoform X1

  2. XM_011537066.2XP_011535368.1  spermatogenesis-defective protein 39 homolog isoform X1

    Conserved Domains (1) summary
    pfam09787
    Location:26440
    Golgin_A5; Golgin subfamily A member 5
  3. XM_017021581.2XP_016877070.1  spermatogenesis-defective protein 39 homolog isoform X2

  4. XM_017021580.2XP_016877069.1  spermatogenesis-defective protein 39 homolog isoform X2

RNA

  1. XR_001750501.2 RNA Sequence

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