vps4b vacuolar protein sorting 4 homolog B [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: vps4bprovided by ZNC
Official Full Name: vacuolar protein sorting 4 homolog Bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-1235
See related: Ensembl:ENSDARG00000069175 AllianceGenome:ZFIN:ZDB-GENE-040426-1235
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zgc:63682; ch73-81e6.1
Summary: Predicted to enable ATP hydrolysis activity. Acts upstream of or within odontogenesis. Predicted to be located in late endosome membrane. Is expressed in ceratobranchial 5 primary tooth; pharyngeal arch 3-7; and pharyngeal pouch. Orthologous to human VPS4B (vacuolar protein sorting 4 homolog B). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 2

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (13255986..13333934, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (13573200..13651169, complement)

Chromosome 2 - NC_007113.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within odontogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 4B

Names: vacuolar protein sorting 4 homolog b-like; vacuolar protein sorting 4b homolog B

NP_001094432.1

EC 3.6.4.6

NP_001278351.1

EC 3.6.4.6

XP_009296349.1

EC 3.6.4.6

XP_009296350.1

EC 3.6.4.6

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)

NM_001100962.1 → NP_001094432.1 vacuolar protein sorting-associated protein 4B

See identical proteins and their annotated locations for NP_001094432.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' UTR compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

CU207344

UniProtKB/TrEMBL

A0A8M1P1A0, A5WWM0

Related

ENSDARP00000074209.5, ENSDART00000079757.6

Conserved Domains (5) summary

smart00382
Location:159 → 295

AAA; ATPases associated with a variety of cellular activities

cd02678
Location:5 → 68

MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.

pfam00004
Location:163 → 293

AAA; ATPase family associated with various cellular activities (AAA)

pfam09336
Location:374 → 434

Vps4_C; Vps4 C terminal oligomerization domain

cl21455
Location:128 → 182

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
NM_001291422.1 → NP_001278351.1 vacuolar protein sorting-associated protein 4B

See identical proteins and their annotated locations for NP_001278351.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

CU207344

UniProtKB/TrEMBL

A0A8M1P1A0, A5WWM0

Related

ENSDARP00000111799.2, ENSDART00000127693.4

Conserved Domains (5) summary

smart00382
Location:159 → 295

AAA; ATPases associated with a variety of cellular activities

cd02678
Location:5 → 68

MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.

pfam00004
Location:163 → 293

AAA; ATPase family associated with various cellular activities (AAA)

pfam09336
Location:374 → 434

Vps4_C; Vps4 C terminal oligomerization domain

cl21455
Location:128 → 182

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007113.7 Reference GRCz11 Primary Assembly

Range

13255986..13333934 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009298075.4 → XP_009296350.1 vacuolar protein sorting-associated protein 4B isoform X2

UniProtKB/TrEMBL

A0A0R4IPK7, A0A8M3AWN2

Related

ENSDARP00000136647.1, ENSDART00000168258.2

Conserved Domains (5) summary

smart00382
Location:229 → 365

AAA; ATPases associated with a variety of cellular activities

pfam00004
Location:233 → 363

AAA; ATPase family associated with various cellular activities (AAA)

pfam09336
Location:444 → 504

Vps4_C; Vps4 C terminal oligomerization domain

cl00299
Location:75 → 138

MIT; MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar ...

cl21455
Location:198 → 252

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
XM_009298074.4 → XP_009296349.1 vacuolar protein sorting-associated protein 4B isoform X1

UniProtKB/TrEMBL

A0A8M3AZR5

Conserved Domains (6) summary

smart00382
Location:237 → 373

AAA; ATPases associated with a variety of cellular activities

COG0457
Location:8 → 118

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

pfam00004
Location:241 → 371

AAA; ATPase family associated with various cellular activities (AAA)

pfam09336
Location:452 → 512

Vps4_C; Vps4 C terminal oligomerization domain

cl00299
Location:86 → 146

MIT; MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar ...

cl21455
Location:206 → 260

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases