ddx46 DEAD (Asp-Glu-Ala-Asp) box polypeptide 46 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: ddx46provided by ZNC
Official Full Name: DEAD (Asp-Glu-Ala-Asp) box polypeptide 46provided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-667
See related: Ensembl:ENSDARG00000099458 AllianceGenome:ZFIN:ZDB-GENE-030131-667
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: fb39a03; fj67d06; wu:fb39a03; wu:fj67d06
Summary: Predicted to enable several functions, including ATP binding activity; RNA binding activity; and RNA helicase activity. Acts upstream of or within several processes, including animal organ development; mRNA splicing, via spliceosome; and positive regulation of cell differentiation. Predicted to be located in Cajal body and nuclear speck. Predicted to be active in nucleus. Is expressed in brain; digestive system; head; hematopoietic system; and pectoral fin bud. Orthologous to human DDX46 (DEAD-box helicase 46). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 21

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	21	NC_007132.7 (45717830..45732179)
105	previous assembly	GRCz10 (GCF_000002035.5)	21	NC_007132.6 (45575505..45589810, complement)

Chromosome 21 - NC_007132.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

zebrafish Ddx46 is required for the multilineage differentiation of hematopoietic stem cells during development, through the regulation of specific gene expressions.
Title: Ddx46 is required for multi-lineage differentiation of hematopoietic stem cells in zebrafish.
a model in which zebrafish Ddx46 is required for the development of the digestive organs and brain, possibly through the control of pre-mRNA splicing.
Title: DEAD-box protein Ddx46 is required for the development of the digestive organs and brain in zebrafish.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G46485 (e-PCR)
- UniSTS:107287

fb39a03.x1 (e-PCR)
- UniSTS:190553

fj67d06.x1 (e-PCR)
- UniSTS:199827

fa11g02.s1 (e-PCR)
- UniSTS:189587

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 RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	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 RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in U2-type prespliceosome assembly	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within definitive hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within digestive tract morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within exocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within liver morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of hematopoietic stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of lymphocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Cajal body	IEA Inferred from Electronic Annotation more info
part_of U2-type spliceosomal complex	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of spliceosomal complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: probable ATP-dependent RNA helicase DDX46

Names: DEAD box protein 46

NP_001019988.1

EC 3.6.4.13

XP_009294012.1

EC 3.6.4.13

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_001024817.1 → NP_001019988.1 probable ATP-dependent RNA helicase DDX46

See identical proteins and their annotated locations for NP_001019988.1

Status: PROVISIONAL

Source sequence(s)

DQ054379

UniProtKB/Swiss-Prot

Q4TVV3

Related

ENSDARP00000135125.1, ENSDART00000164315.2

Conserved Domains (3) summary

smart00487
Location:355 → 564

DEXDc; DEAD-like helicases superfamily

cd00079
Location:560 → 690

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

cd00268
Location:346 → 549

DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007132.7 Reference GRCz11 Primary Assembly

Range

45717830..45732179

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009295737.3 → XP_009294012.1 probable ATP-dependent RNA helicase DDX46 isoform X1

UniProtKB/TrEMBL

A0A8M3AX96

Conserved Domains (3) summary

COG0513
Location:348 → 811

SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

cd00079
Location:577 → 707

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

cd00268
Location:363 → 566

DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...