bmal1a basic helix-loop-helix ARNT like 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: bmal1aprovided by ZNC
Official Full Name: basic helix-loop-helix ARNT like 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-000509-1
See related: Ensembl:ENSDARG00000006791 AllianceGenome:ZFIN:ZDB-GENE-000509-1
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: bmal1; arntl1a; zfBMAL1; wu:fa04g03
Summary: Enables transcription cis-regulatory region binding activity. Contributes to DNA binding activity. Acts upstream of or within several processes, including photoperiodism; regulation of DNA-templated transcription; and regulation of vasculature development. Part of transcription regulator complex. Human ortholog(s) of this gene implicated in alcohol dependence and bipolar disorder. Orthologous to human BMAL1 (basic helix-loop-helix ARNT like 1). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: all
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Genomic context

Location:: chromosome: 25

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	25	NC_007136.7 (17893783..17918853, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	25	NC_007136.6 (17797384..17822457, complement)

Chromosome 25 - NC_007136.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

At the molecular level, we show that the circadian regulator Bmal1 directly targets the promoter region of the vegf gene in zebrafish, leading to an elevated expression of VEGF.
Title: Clock controls angiogenesis.
Opposing effects of circadian clock genes bmal1 and period2 in regulation of VEGF-dependent angiogenesis in developing zebrafish.
Title: Opposing effects of circadian clock genes bmal1 and period2 in regulation of VEGF-dependent angiogenesis in developing zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

fi77f10.y1 (e-PCR)
- UniSTS:198038

fa04g03.s1 (e-PCR)
- UniSTS:202201

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
contributes_to DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in circadian rhythm	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within circadian rhythm	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within photoperiodism	IEP Inferred from Expression Pattern more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of vasculature development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of vasculature development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to light stimulus	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in PML body	IEA Inferred from Electronic Annotation more info
part_of aryl hydrocarbon receptor complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	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 protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: basic helix-loop-helix ARNT like 1a

Names: aryl hydrocarbon receptor nuclear translocator-like 1a; brain and muscle ARNT-like 1; hif1b

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_131577.1 → NP_571652.1 basic helix-loop-helix ARNT like 1a

See identical proteins and their annotated locations for NP_571652.1

Status: PROVISIONAL

Source sequence(s)

AF144689

UniProtKB/TrEMBL

Q78CJ2, Q9I879

Related

ENSDARP00000124722.1, ENSDART00000148660.3

Conserved Domains (5) summary

smart00091
Location:153 → 212

PAS; PAS domain

cd00130
Location:345 → 440

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00010
Location:78 → 130

HLH; Helix-loop-helix DNA-binding domain

pfam00989
Location:150 → 257

PAS; PAS fold

pfam14598
Location:343 → 446

PAS_11; PAS domain

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_007136.7 Reference GRCz11 Primary Assembly

Range

17893783..17918853 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005163022.5 → XP_005163079.1 basic helix-loop-helix ARNT like 1a isoform X1

See identical proteins and their annotated locations for XP_005163079.1

UniProtKB/TrEMBL

Q78CJ2, Q9I879

Related

ENSDARP00000004223.9, ENSDART00000023959.10

Conserved Domains (5) summary

smart00091
Location:153 → 212

PAS; PAS domain

cd00130
Location:345 → 440

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00010
Location:78 → 130

HLH; Helix-loop-helix DNA-binding domain

pfam00989
Location:150 → 257

PAS; PAS fold

pfam14598
Location:343 → 446

PAS_11; PAS domain