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

Gene ID: 64067, updated on 19-Sep-2024

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; AllianceGenome:HGNC:19311
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
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Genomic context

See NPAS3 in Genome Data Viewer
Location:
14q13.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (32934785..33804173)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (27131685..28001533)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (33408085..34273379)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 11725 Neighboring gene A-kinase anchoring protein 6 Neighboring gene MT-CO1 pseudogene 2 Neighboring gene uncharacterized LOC124903298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8241 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:33281639-33282368 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:33282369-33283098 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:33603289-33603866 Neighboring gene NANOG hESC enhancer GRCh37_chr14:33922151-33922707 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:33944722-33945332 Neighboring gene NANOG hESC enhancer GRCh37_chr14:33946898-33947463 Neighboring gene uncharacterized LOC124903299 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:34021175-34021810 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:34033742-34034271 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:34081250-34081760 Neighboring gene uncharacterized LOC124903300 Neighboring gene Sharpr-MPRA regulatory region 868 Neighboring gene small nucleolar RNA, H/ACA box 89 Neighboring gene Sharpr-MPRA regulatory region 9495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:34366891-34367394 Neighboring gene GATA motif-containing MPRA enhancer 110 Neighboring gene NANOG hESC enhancer GRCh37_chr14:34400622-34401183 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:34407170-34408141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5660 Neighboring gene uncharacterized LOC102724945 Neighboring gene uncharacterized LOC105370446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:34433111-34433612 Neighboring gene egl-9 family hypoxia inducible factor 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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?

Phenotypes

EBI GWAS Catalog

Description
A genome-wide association meta-analysis of plasma Aβ peptides concentrations in the elderly.
EBI GWAS Catalog
A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
EBI GWAS Catalog
A genome-wide association study in the genetic analysis of idiopathic thrombophilia project suggests sex-specific regulation of mitochondrial DNA levels.
EBI GWAS 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.
EBI GWAS Catalog
Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder.
EBI GWAS Catalog
Cross-disorder genomewide analysis of schizophrenia, bipolar disorder, and depression.
EBI GWAS Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ10003, FLJ11138, FLJ11605

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 ISA
Inferred from Sequence Alignment
more info
 
enables RNA polymerase II transcription 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 heterodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 

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)

NEW Try the new Transcript table

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
    4627..869921
    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
    Q86US6, Q86US7, Q8IXF0, Q8IXF2, Q9BY81, Q9H323, Q9Y4L8
    UniProtKB/TrEMBL
    X5D2Q4, X5DNV7
    Related
    ENSP00000348460.4, ENST00000356141.9
    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/TrEMBL
    X5D988, X5DNV7
    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_001394988.1NP_001381917.1  neuronal PAS domain-containing protein 3 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL109769, AL139296, AL157689, AL158802, AL161851
    UniProtKB/TrEMBL
    X5DR67
    Conserved Domains (4) summary
    smart00091
    Location:137195
    PAS; PAS domain
    pfam08447
    Location:328415
    PAS_3; PAS fold
    cd19732
    Location:1794
    bHLH-PAS_NPAS3_PASD6; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 3 (NPAS3) and similar proteins
    NF033845
    Location:455580
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
  4. NM_001394989.1NP_001381918.1  neuronal PAS domain-containing protein 3 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL109769, AL139296, AL157689, AL158802, AL161851
    UniProtKB/TrEMBL
    X5D7M0, X5DNV7
    Conserved Domains (4) summary
    smart00091
    Location:122180
    PAS; PAS domain
    pfam08447
    Location:313400
    PAS_3; PAS fold
    cd19732
    Location:1794
    bHLH-PAS_NPAS3_PASD6; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 3 (NPAS3) and similar proteins
    NF033845
    Location:440562
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
  5. 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/TrEMBL
    X5DNV7
    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
  6. 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/TrEMBL
    X5DR67
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    32934785..33804173
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021582.2XP_016877071.1  neuronal PAS domain-containing protein 3 isoform X1

    UniProtKB/TrEMBL
    F8VR32
  2. XM_017021583.2XP_016877072.1  neuronal PAS domain-containing protein 3 isoform X3

    UniProtKB/TrEMBL
    F8VS42
  3. XM_047431678.1XP_047287634.1  neuronal PAS domain-containing protein 3 isoform X2

    UniProtKB/TrEMBL
    F8VR32
  4. XM_005267991.4XP_005268048.2  neuronal PAS domain-containing protein 3 isoform X4

    UniProtKB/TrEMBL
    F8VR32
  5. XM_011537069.3XP_011535371.2  neuronal PAS domain-containing protein 3 isoform X6

    UniProtKB/TrEMBL
    F8VS42
  6. XM_017021584.2XP_016877073.1  neuronal PAS domain-containing protein 3 isoform X7

    UniProtKB/TrEMBL
    F8VS42
  7. XM_017021585.2XP_016877074.1  neuronal PAS domain-containing protein 3 isoform X9

    UniProtKB/TrEMBL
    F8VS42
  8. XM_005267992.4XP_005268049.2  neuronal PAS domain-containing protein 3 isoform X5

    UniProtKB/TrEMBL
    F8VR32
    Related
    ENSP00000450392.1, ENST00000551492.5
  9. XM_011537071.3XP_011535373.2  neuronal PAS domain-containing protein 3 isoform X10

    UniProtKB/TrEMBL
    F8VS42
    Related
    ENSP00000448373.2, ENST00000551634.6
  10. XM_011537067.3XP_011535369.1  neuronal PAS domain-containing protein 3 isoform X8

    UniProtKB/TrEMBL
    X5DR67
    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
  11. XM_047431680.1XP_047287636.1  neuronal PAS domain-containing protein 3 isoform X11

    UniProtKB/TrEMBL
    X5DNV7
  12. XM_017021588.2XP_016877077.1  neuronal PAS domain-containing protein 3 isoform X12

    UniProtKB/TrEMBL
    X5D985
    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_017021587.2XP_016877076.1  neuronal PAS domain-containing protein 3 isoform X12

    UniProtKB/TrEMBL
    X5D985
    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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    27131685..28001533
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376560.1XP_054232535.1  neuronal PAS domain-containing protein 3 isoform X1

    UniProtKB/TrEMBL
    F8VR32
  2. XM_054376562.1XP_054232537.1  neuronal PAS domain-containing protein 3 isoform X3

    UniProtKB/TrEMBL
    F8VS42
  3. XM_054376561.1XP_054232536.1  neuronal PAS domain-containing protein 3 isoform X2

    UniProtKB/TrEMBL
    F8VR32
  4. XM_054376563.1XP_054232538.1  neuronal PAS domain-containing protein 3 isoform X4

    UniProtKB/TrEMBL
    F8VR32
  5. XM_054376565.1XP_054232540.1  neuronal PAS domain-containing protein 3 isoform X6

    UniProtKB/TrEMBL
    F8VS42
  6. XM_054376566.1XP_054232541.1  neuronal PAS domain-containing protein 3 isoform X7

    UniProtKB/TrEMBL
    F8VS42
  7. XM_054376568.1XP_054232543.1  neuronal PAS domain-containing protein 3 isoform X9

    UniProtKB/TrEMBL
    F8VS42
  8. XM_054376564.1XP_054232539.1  neuronal PAS domain-containing protein 3 isoform X5

    UniProtKB/TrEMBL
    F8VR32
  9. XM_054376569.1XP_054232544.1  neuronal PAS domain-containing protein 3 isoform X10

    UniProtKB/TrEMBL
    F8VS42
  10. XM_054376567.1XP_054232542.1  neuronal PAS domain-containing protein 3 isoform X8

    UniProtKB/TrEMBL
    X5DR67
  11. XM_054376570.1XP_054232545.1  neuronal PAS domain-containing protein 3 isoform X11

    UniProtKB/TrEMBL
    X5DNV7
  12. XM_054376572.1XP_054232547.1  neuronal PAS domain-containing protein 3 isoform X12

    UniProtKB/TrEMBL
    X5D985
  13. XM_054376571.1XP_054232546.1  neuronal PAS domain-containing protein 3 isoform X12

    UniProtKB/TrEMBL
    X5D985