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ARNTL2 aryl hydrocarbon receptor nuclear translocator like 2 [ Homo sapiens (human) ]

Gene ID: 56938, updated on 12-Oct-2019

Summary

Official Symbol
ARNTL2provided by HGNC
Official Full Name
aryl hydrocarbon receptor nuclear translocator like 2provided by HGNC
Primary source
HGNC:HGNC:18984
See related
Ensembl:ENSG00000029153 MIM:614517
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
CLIF; MOP9; BMAL2; PASD9; bHLHe6
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, Oct 2011]
Expression
Broad expression in esophagus (RPKM 6.4), appendix (RPKM 3.2) and 17 other tissues See more
Orthologs

Genomic context

See ARNTL2 in Genome Data Viewer
Location:
12p11.23
Exon count:
20
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (27332836..27425813)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (27485787..27578746)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene nontranscribed chromatin-defined enhancer upstream of C12orf71 Neighboring gene serine/threonine kinase 38 like Neighboring gene ARNTL2 antisense RNA 1 Neighboring gene single-pass membrane protein with coiled-coil domains 2 Neighboring gene arginyl-tRNA synthetase 1 pseudogene 1 Neighboring gene PPFIA binding protein 1 Neighboring gene uncharacterized protein C12orf71-like

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?

Pathways from BioSystems

  • BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystem (from REACTOME)
    BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystemAs inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et...
  • Circadian Clock, organism-specific biosystem (from REACTOME)
    Circadian Clock, organism-specific biosystemAt the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by b...
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC149671, MGC149672

Gene Ontology Provided by GOA

Process Evidence Code Pubs
circadian rhythm IDA
Inferred from Direct Assay
more info
PubMed 
entrainment of circadian clock NAS
Non-traceable Author Statement
more info
PubMed 
positive regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
aryl hydrocarbon receptor nuclear translocator-like protein 2
Names
CYCLE-like factor
PAS domain-containing protein 9
basic-helix-loop-helix-PAS protein MOP9
brain and muscle ARNT-like 2
class E basic helix-loop-helix protein 6
member of PAS protein 9
transcription factor BMAL2

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_030359.2 RefSeqGene

    Range
    4983..97960
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001248002.2NP_001234931.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001234931.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AC068794, AC092829, AF246961, AF256215, BQ774827, CV388040
    Consensus CDS
    CCDS58219.1
    UniProtKB/Swiss-Prot
    Q8WYA1
    Related
    ENSP00000312247.5, ENST00000311001.9
    Conserved Domains (4) summary
    cd00130
    Location:356454
    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:95147
    HLH; Helix-loop-helix DNA-binding domain
    pfam00989
    Location:167273
    PAS; PAS fold
    pfam14598
    Location:356458
    PAS_11; PAS domain
  2. NM_001248003.2NP_001234932.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform 3

    See identical proteins and their annotated locations for NP_001234932.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame donor splice site, and lacks two consecutive in-frame coding exons compared to variant 1. This results in a shorter isoform (3) compared to isoform 1.
    Source sequence(s)
    AC068794, AC092829, AF246962, AF256215, BQ774827, CV388040
    Consensus CDS
    CCDS58221.1
    UniProtKB/Swiss-Prot
    Q8WYA1
    Related
    ENSP00000379238.2, ENST00000395901.6
    Conserved Domains (3) summary
    cd00130
    Location:155250
    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:73124
    HLH; Helix-loop-helix DNA-binding domain
    cl25986
    Location:333435
    PAS_3; PAS fold
  3. NM_001248004.2NP_001234933.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform 4

    See identical proteins and their annotated locations for NP_001234933.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two consecutive in-frame coding exons compared to variant 1. This results in a shorter isoform (4) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AC068794, AC092829, AF246963, AF256215, BQ774827, CV388040
    Consensus CDS
    CCDS58220.1
    UniProtKB/Swiss-Prot
    Q8WYA1
    Related
    ENSP00000261178.5, ENST00000261178.9
    Conserved Domains (3) summary
    cd00130
    Location:144239
    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:62113
    HLH; Helix-loop-helix DNA-binding domain
    cl25986
    Location:322424
    PAS_3; PAS fold
  4. NM_001248005.2NP_001234934.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame donor splice site, lacks two consecutive in-frame coding exons, and another exon in the 3' region that causes a frame-shift, compared to variant 1. This results in a shorter isoform (3) with a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC068794, AC092829, AF246960, AF256215, AK296706, BQ774827, CV388040
    Consensus CDS
    CCDS58222.1
    UniProtKB/Swiss-Prot
    Q8WYA1
    Related
    ENSP00000438545.1, ENST00000546179.5
    Conserved Domains (4) summary
    cd00083
    Location:72124
    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:333431
    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:144250
    PAS; PAS fold
    pfam14598
    Location:333435
    PAS_11; PAS domain
  5. NM_020183.5NP_064568.3  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform 1

    See identical proteins and their annotated locations for NP_064568.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC068794, AC092829, AF246960, AF256215, BQ774827, CV388040
    Consensus CDS
    CCDS8712.1
    UniProtKB/Swiss-Prot
    Q8WYA1
    Related
    ENSP00000266503.5, ENST00000266503.9
    Conserved Domains (4) summary
    cd00130
    Location:370468
    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:109161
    HLH; Helix-loop-helix DNA-binding domain
    pfam00989
    Location:181287
    PAS; PAS fold
    pfam14598
    Location:370472
    PAS_11; PAS domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    27332836..27425813
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520768.2XP_011519070.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X4

    Conserved Domains (3) summary
    cd00130
    Location:350448
    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:120172
    HLH; Helix-loop-helix DNA-binding domain
    pfam14598
    Location:350452
    PAS_11; PAS domain
  2. XM_011520766.2XP_011519068.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X1

    Conserved Domains (4) summary
    cd00130
    Location:381479
    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:120172
    HLH; Helix-loop-helix DNA-binding domain
    pfam00989
    Location:192298
    PAS; PAS fold
    pfam14598
    Location:381483
    PAS_11; PAS domain
  3. XM_006719112.3XP_006719175.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X3

    Related
    ENSP00000400185.2, ENST00000457040.6
    Conserved Domains (4) summary
    cd00130
    Location:367465
    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:106158
    HLH; Helix-loop-helix DNA-binding domain
    pfam00989
    Location:178284
    PAS; PAS fold
    pfam14598
    Location:367469
    PAS_11; PAS domain
  4. XM_011520769.2XP_011519071.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X5

    Related
    ENSP00000442438.1, ENST00000544915.5
    Conserved Domains (4) summary
    cd00130
    Location:347445
    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:86138
    HLH; Helix-loop-helix DNA-binding domain
    pfam00989
    Location:158264
    PAS; PAS fold
    pfam14598
    Location:347449
    PAS_11; PAS domain
  5. XM_017019667.1XP_016875156.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X8

    Conserved Domains (4) summary
    cd00083
    Location:659
    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:268366
    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:79185
    PAS; PAS fold
    pfam14598
    Location:268370
    PAS_11; PAS domain
  6. XM_017019666.1XP_016875155.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X7

  7. XM_024449071.1XP_024304839.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X2

    Conserved Domains (3) summary
    cd00130
    Location:194289
    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:111163
    HLH; Helix-loop-helix DNA-binding domain
    cl25986
    Location:372474
    PAS_3; PAS fold
  8. XM_024449072.1XP_024304840.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X6

    Conserved Domains (3) summary
    cd00130
    Location:146241
    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:64115
    HLH; Helix-loop-helix DNA-binding domain
    cl25986
    Location:324426
    PAS_3; PAS fold
  9. XM_011520770.2XP_011519072.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X8

    See identical proteins and their annotated locations for XP_011519072.1

    Conserved Domains (4) summary
    cd00083
    Location:659
    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:268366
    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:79185
    PAS; PAS fold
    pfam14598
    Location:268370
    PAS_11; PAS domain
  10. XM_017019668.1XP_016875157.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X8

    Conserved Domains (4) summary
    cd00083
    Location:659
    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:268366
    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:79185
    PAS; PAS fold
    pfam14598
    Location:268370
    PAS_11; PAS domain
  11. XM_006719114.3XP_006719177.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X10

    Conserved Domains (4) summary
    smart00353
    Location:139
    HLH; helix loop helix domain
    cd00130
    Location:248346
    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:59165
    PAS; PAS fold
    pfam14598
    Location:248350
    PAS_11; PAS domain
  12. XM_011520771.2XP_011519073.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X8

    See identical proteins and their annotated locations for XP_011519073.1

    Conserved Domains (4) summary
    cd00083
    Location:659
    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:268366
    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:79185
    PAS; PAS fold
    pfam14598
    Location:268370
    PAS_11; PAS domain
  13. XM_017019669.1XP_016875158.1  aryl hydrocarbon receptor nuclear translocator-like protein 2 isoform X9

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