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NPAS3 neuronal PAS domain protein 3 [ Homo sapiens (human) ]

Gene ID: 64067, updated on 17-Jun-2019

Summary

Official Symbol
NPAS3provided by HGNC
Official Full Name
neuronal PAS domain protein 3provided by HGNC
Primary source
HGNC:HGNC:19311
See related
Ensembl:ENSG00000151322 MIM:609430
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
MOP6; PASD6; bHLHe12
Summary
This gene encodes a member of the basic helix-loop-helix and PAS domain-containing family of transcription factors. The encoded protein is localized to the nucleus and may regulate genes involved in neurogenesis. Chromosomal abnormalities that affect the coding potential of this gene are associated with schizophrenia and cognitive disability. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
Expression
Biased expression in brain (RPKM 3.9), endometrium (RPKM 1.3) and 4 other tissues See more
Orthologs

Genomic context

See NPAS3 in Genome Data Viewer
Location:
14q13.1
Exon count:
18
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (32934785..33804176)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (33404115..34273382)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene A-kinase anchoring protein 6 Neighboring gene MT-CO1 pseudogene 2 Neighboring gene uncharacterized LOC112268128 Neighboring gene uncharacterized LOC105370443 Neighboring gene small nucleolar RNA, H/ACA box 89 Neighboring gene GATA motif-containing MPRA enhancer 110 Neighboring gene egl-9 family hypoxia inducible factor 3

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association meta-analysis of plasma Aβ peptides concentrations in the elderly.
NHGRI GWA Catalog
A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
NHGRI GWA Catalog
A genome-wide association study in the genetic analysis of idiopathic thrombophilia project suggests sex-specific regulation of mitochondrial DNA levels.
NHGRI GWA Catalog
A genome-wide association study of inflammatory biomarker changes in response to fenofibrate treatment in the Genetics of Lipid Lowering Drug and Diet Network.
NHGRI GWA Catalog
Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder.
NHGRI GWA Catalog
Cross-disorder genomewide analysis of schizophrenia, bipolar disorder, and depression.
NHGRI GWA Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10003, FLJ11138, FLJ11605

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
protein heterodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
neuronal PAS domain-containing protein 3
Names
PAS domain-containing protein 6
basic-helix-loop-helix-PAS protein MOP6
class E basic helix-loop-helix protein 12
member of PAS protein 6
neuronal PAS3

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_013036.2 RefSeqGene

    Range
    5001..869924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001164749.2NP_001158221.1  neuronal PAS domain-containing protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001158221.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB055962, AI811363, AL109769, AL157689, AY157302
    Consensus CDS
    CCDS53891.1
    UniProtKB/Swiss-Prot
    Q8IXF0
    UniProtKB/TrEMBL
    X5D2Q4
    Related
    ENSP00000348460.4, ENST00000356141.8
    Conserved Domains (5) summary
    smart00091
    Location:152210
    PAS; PAS domain
    cd00083
    Location:52109
    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:331413
    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:152210
    PAS; PAS fold
    pfam08447
    Location:343430
    PAS_3; PAS fold
  2. NM_001165893.2NP_001159365.1  neuronal PAS domain-containing protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001159365.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AB054575, AI811363, AL109769, AL157689
    Consensus CDS
    CCDS55912.1
    UniProtKB/Swiss-Prot
    Q8IXF0
    UniProtKB/TrEMBL
    X5D988
    Related
    ENSP00000448916.1, ENST00000548645.5
    Conserved Domains (5) summary
    smart00091
    Location:122180
    PAS; PAS domain
    cd00083
    Location:2279
    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:301383
    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:122180
    PAS; PAS fold
    pfam08447
    Location:313400
    PAS_3; PAS fold
  3. NM_022123.3NP_071406.1  neuronal PAS domain-containing protein 3 isoform 2

    See identical proteins and their annotated locations for NP_071406.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AF164438, AI811363, AL109769, AL157689
    Consensus CDS
    CCDS9645.1
    UniProtKB/Swiss-Prot
    Q8IXF0
    Related
    ENSP00000319610.5, ENST00000346562.6
    Conserved Domains (5) summary
    smart00091
    Location:120178
    PAS; PAS domain
    cd00083
    Location:2279
    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:299381
    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:120178
    PAS; PAS fold
    pfam08447
    Location:311398
    PAS_3; PAS fold
  4. NM_173159.3NP_775182.1  neuronal PAS domain-containing protein 3 isoform 3

    See identical proteins and their annotated locations for NP_775182.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 3, which is shorter than isoform 1.
    Source sequence(s)
    AB054576, AF164438, AI811363, AL109769, AL157689
    Consensus CDS
    CCDS53892.1
    UniProtKB/Swiss-Prot
    Q8IXF0
    Related
    ENSP00000350446.5, ENST00000357798.9
    Conserved Domains (5) summary
    smart00091
    Location:139197
    PAS; PAS domain
    cd00083
    Location:2279
    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:318400
    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:139197
    PAS; PAS fold
    pfam08447
    Location:330417
    PAS_3; PAS fold

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    32934785..33804176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021582.1XP_016877071.1  neuronal PAS domain-containing protein 3 isoform X1

  2. XM_017021583.1XP_016877072.1  neuronal PAS domain-containing protein 3 isoform X2

  3. XM_005267991.3XP_005268048.2  neuronal PAS domain-containing protein 3 isoform X3

  4. XM_011537069.2XP_011535371.2  neuronal PAS domain-containing protein 3 isoform X5

  5. XM_017021584.1XP_016877073.1  neuronal PAS domain-containing protein 3 isoform X6

  6. XM_017021585.1XP_016877074.1  neuronal PAS domain-containing protein 3 isoform X8

  7. XM_005267992.3XP_005268049.2  neuronal PAS domain-containing protein 3 isoform X4

    Related
    ENSP00000450392.1, ENST00000551492.5
  8. XM_011537071.2XP_011535373.2  neuronal PAS domain-containing protein 3 isoform X9

    Related
    ENSP00000448373.1, ENST00000551634.5
  9. XM_011537067.2XP_011535369.1  neuronal PAS domain-containing protein 3 isoform X7

    Conserved Domains (5) summary
    smart00091
    Location:169227
    PAS; PAS domain
    cd00083
    Location:52109
    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:348430
    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:169227
    PAS; PAS fold
    pfam08447
    Location:360447
    PAS_3; PAS fold
  10. XM_011537070.2XP_011535372.1  neuronal PAS domain-containing protein 3 isoform X10

    Conserved Domains (5) summary
    smart00091
    Location:137195
    PAS; PAS domain
    cd00083
    Location:2279
    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:316398
    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:137195
    PAS; PAS fold
    pfam08447
    Location:328415
    PAS_3; PAS fold
  11. XM_011537072.2XP_011535374.1  neuronal PAS domain-containing protein 3 isoform X11

    See identical proteins and their annotated locations for XP_011535374.1

    UniProtKB/TrEMBL
    X5D7M0
    Conserved Domains (5) summary
    smart00091
    Location:122180
    PAS; PAS domain
    cd00083
    Location:2279
    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:301383
    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:122180
    PAS; PAS fold
    pfam08447
    Location:313400
    PAS_3; PAS fold
  12. XM_017021586.1XP_016877075.1  neuronal PAS domain-containing protein 3 isoform X12

    Conserved Domains (4) summary
    smart00091
    Location:50108
    PAS; PAS domain
    cd00130
    Location:229311
    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:50108
    PAS; PAS fold
    pfam08447
    Location:241328
    PAS_3; PAS fold
  13. XM_017021588.1XP_016877077.1  neuronal PAS domain-containing protein 3 isoform X12

    Conserved Domains (4) summary
    smart00091
    Location:50108
    PAS; PAS domain
    cd00130
    Location:229311
    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:50108
    PAS; PAS fold
    pfam08447
    Location:241328
    PAS_3; PAS fold
  14. XM_017021587.1XP_016877076.1  neuronal PAS domain-containing protein 3 isoform X12

    Conserved Domains (4) summary
    smart00091
    Location:50108
    PAS; PAS domain
    cd00130
    Location:229311
    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:50108
    PAS; PAS fold
    pfam08447
    Location:241328
    PAS_3; PAS fold
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