Bmal2 basic helix-loop-helix ARNT like 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Bmal2provided by MGI
Official Full Name: basic helix-loop-helix ARNT like 2provided by MGI
Primary source: MGI:MGI:2684845
See related: Ensembl:ENSMUSG00000040187 AllianceGenome:MGI:2684845
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: CLIF; MOP9; Arntl2; bHLHe6; 4632430A05Rik
Summary: This gene encodes a basic helix-loop-helix transcription factor belonging to the PAS (Per, Arnt, Sim) superfamily. The PAS proteins play important roles in adaptation to low atmospheric and cellular oxygen levels, exposure to certain environmental pollutants, and diurnal oscillations in light and temperature. This protein forms a transcriptionally active heterodimer with the circadian Clock protein, the structurally related Mop4, and hypoxia-inducible factors, such as Hif1alpha. Consistent with its role as a biologically relevant partner of circadian and hypoxia factors, this protein is coexpressed in regions of the brain such as the thalamus, hypothalamus, and amygdala. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2014]
Expression: Broad expression in bladder adult (RPKM 3.7), cortex adult (RPKM 2.2) and 21 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 G3; 6 77.7 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (146696230..146735027)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (146794729..146833529)

Chromosome 6 - NC_000072.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Our results identify Arntl2 as a gene controlling thymocyte apoptosis and proliferation along with Th17 development through the IL-21 pathway.
Title: The circadian gene Arntl2 on distal mouse chromosome 6 controls thymocyte apoptosis.
Our results describe a novel and rather unexpected role for Arntl2 in the immune system that lies outside of its predicted function in circadian rhythm regulation
Title: Linking the circadian rhythm gene Arntl2 to interleukin 21 expression in type 1 diabetes.
Results provide additional support for the protective role of the Arntl2 gene located in locus Idd6 in diabetes progression in NOD.C3H congenic mice.
Title: Downregulation of the circadian rhythm related gene Arntl2 suppresses diabetes protection in Idd6 NOD.C3H congenic mice.
Expression of Bmal2 can rescue the clock and metabolic phenotypes of Bmal1-knockout mice, including rhythmic locomotor activity, rhythmic metabolism, low body weight, and enhanced fat deposition.
Title: Circadian clock gene Bmal1 is not essential; functional replacement with its paralog, Bmal2.
PER2 is inhibited by BMAL2-CLOCK, which reemphasizes its negative role and a positive role of BMAL2 in circadian transcription
Title: Preferential inhibition of BMAL2-CLOCK activity by PER2 reemphasizes its negative role and a positive role of BMAL2 in the circadian transcription.
These findings demonstrate that (57)Arg in the basic region of DEC2 is essential for its activity in suppressing CLOCK/BMAL2-mediated transactivation.
Title: 57Arg in the bHLH transcription factor DEC2 is essential for the suppression of CLOCK/BMAL2-mediated transactivation.
Arntl2 exhibited a six-fold upregulation in spleens of the NOD.C3H 6.VIII congenic strain compared with the NOD control strain, strain-specific splice variants and a large number of polymorphisms in both coding and non-coding regions.
Title: Identification of the transcription factor ARNTL2 as a candidate gene for the type 1 diabetes locus Idd6.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (1)

General gene information

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Markers

NoName (e-PCR)
- UniSTS:489532

Arntl2 (e-PCR), detects polymorphism
- UniSTS:547185

Gene Ontology Provided by MGI

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

Process	Evidence Code	Pubs
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in 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 transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of CLOCK-BMAL transcription complex	IPI Inferred from Physical Interaction more info	PubMed
part_of CLOCK-BMAL transcription complex	ISO Inferred from Sequence Orthology 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
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
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 protein 2

Names: aryl hydrocarbon receptor nuclear translocator-like 2; aryl hydrocarbon receptor nuclear translocator-like protein 2; brain and muscle ARNT-like 2; brain-muscle-ARNT-like protein 2

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_001289679.1 → NP_001276608.1 basic helix-loop-helix ARNT-like protein 2 isoform 2

See identical proteins and their annotated locations for NP_001276608.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC164631, AK019506, AY005163, BY604501, DQ322241

Consensus CDS

CCDS80641.1

UniProtKB/TrEMBL

E9Q993, Q1A532

Related

ENSMUSP00000107265.2, ENSMUST00000111638.8

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 401

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
NM_001289680.1 → NP_001276609.1 basic helix-loop-helix ARNT-like protein 2 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AK019506, AY005163, BY604501, DQ355143

Consensus CDS

CCDS80640.1

UniProtKB/TrEMBL

E9Q994, Q1A3C9

Related

ENSMUSP00000107263.2, ENSMUST00000111636.8

Conserved Domains (4) summary

cd00083
Location:50 → 106

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:308 → 407

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 ...

pfam00989
Location:127 → 226

PAS; PAS fold

pfam14598
Location:309 → 411

PAS_11; PAS domain
NM_001289681.1 → NP_001276610.1 basic helix-loop-helix ARNT-like protein 2 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate splice site in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus than isoform 1.

Source sequence(s)

AK019506, AY014836, BY604501

UniProtKB/Swiss-Prot

Q2VPD4

Conserved Domains (1) summary

pfam14598
Location:85 → 187

PAS_11; PAS domain
NM_172309.2 → NP_758513.1 basic helix-loop-helix ARNT-like protein 2 isoform 1

See identical proteins and their annotated locations for NP_758513.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AK019506, AY005163, BY604501

Consensus CDS

CCDS20702.1

UniProtKB/Swiss-Prot

Q2VPD4, Q32MV7, Q91XJ5, Q91XJ6

UniProtKB/TrEMBL

Q1A3C9

Related

ENSMUSP00000079373.5, ENSMUST00000080530.6

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 416

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

146696230..146735027

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017321603.3 → XP_017177092.1 basic helix-loop-helix ARNT-like protein 2 isoform X1

UniProtKB/TrEMBL

Q1A3C9

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 411

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507061.2 → XP_006507124.1 basic helix-loop-helix ARNT-like protein 2 isoform X8

Conserved Domains (1) summary

pfam14598
Location:85 → 187

PAS_11; PAS domain
XM_030255434.1 → XP_030111294.1 basic helix-loop-helix ARNT-like protein 2 isoform X9

Conserved Domains (1) summary

pfam14598
Location:85 → 187

PAS_11; PAS domain
XM_006507055.5 → XP_006507118.1 basic helix-loop-helix ARNT-like protein 2 isoform X5

UniProtKB/TrEMBL

Q1A532

Conserved Domains (3) summary

cd00130
Location:133 → 184

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 ...

pfam14598
Location:309 → 411

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507060.5 → XP_006507123.1 basic helix-loop-helix ARNT-like protein 2 isoform X7

Conserved Domains (3) summary

cd00130
Location:133 → 184

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 ...

pfam14598
Location:309 → 411

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507052.4 → XP_006507115.1 basic helix-loop-helix ARNT-like protein 2 isoform X2

UniProtKB/TrEMBL

Q1A532

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 401

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507049.4 → XP_006507112.1 basic helix-loop-helix ARNT-like protein 2 isoform X1

See identical proteins and their annotated locations for XP_006507112.1

UniProtKB/TrEMBL

Q1A3C9

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 411

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507048.4 → XP_006507111.1 basic helix-loop-helix ARNT-like protein 2 isoform X1

See identical proteins and their annotated locations for XP_006507111.1

UniProtKB/TrEMBL

Q1A3C9

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 411

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507056.4 → XP_006507119.1 basic helix-loop-helix ARNT-like protein 2 isoform X6

UniProtKB/TrEMBL

Q1A3C9

Conserved Domains (3) summary

cd00130
Location:133 → 184

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 ...

pfam14598
Location:309 → 411

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507054.4 → XP_006507117.1 basic helix-loop-helix ARNT-like protein 2 isoform X4

See identical proteins and their annotated locations for XP_006507117.1

UniProtKB/TrEMBL

E9Q993, Q1A532

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 401

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_036166196.1 → XP_036022089.1 basic helix-loop-helix ARNT-like protein 2 isoform X3

UniProtKB/Swiss-Prot

Q2VPD4, Q32MV7, Q91XJ5, Q91XJ6

UniProtKB/TrEMBL

Q1A3C9

Related

ENSMUSP00000107266.2, ENSMUST00000111639.8

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 416

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507053.4 → XP_006507116.1 basic helix-loop-helix ARNT-like protein 2 isoform X3

See identical proteins and their annotated locations for XP_006507116.1

UniProtKB/Swiss-Prot

Q2VPD4, Q32MV7, Q91XJ5, Q91XJ6

UniProtKB/TrEMBL

Q1A3C9

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 416

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_030255433.2 → XP_030111293.1 basic helix-loop-helix ARNT-like protein 2 isoform X8

Conserved Domains (1) summary

pfam14598
Location:85 → 187

PAS_11; PAS domain
XM_006507050.3 → XP_006507113.1 basic helix-loop-helix ARNT-like protein 2 isoform X1

See identical proteins and their annotated locations for XP_006507113.1

UniProtKB/TrEMBL

Q1A3C9

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 411

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily
XM_006507051.5 → XP_006507114.1 basic helix-loop-helix ARNT-like protein 2 isoform X1

See identical proteins and their annotated locations for XP_006507114.1

UniProtKB/TrEMBL

Q1A3C9

Conserved Domains (3) summary

smart00091
Location:125 → 184

PAS; PAS domain

pfam14598
Location:309 → 411

PAS_11; PAS domain

cl00081
Location:49 → 108

bHLH_SF; basic Helix Loop Helix (bHLH) domain superfamily