Npas1 neuronal PAS domain protein 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Npas1provided by RGD
Official Full Name: neuronal PAS domain protein 1provided by RGD
Primary source: RGD:1310040
See related: EnsemblRapid:ENSRNOG00000015376 AllianceGenome:RGD:1310040
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in negative regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within maternal behavior; negative regulation of transcription by RNA polymerase II; and startle response. Predicted to be located in nucleus. Orthologous to human NPAS1 (neuronal PAS domain protein 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 25.7), Kidney (RPKM 3.8) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q21

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (86295509..86316018, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (77167375..77187887, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (78420646..78441841, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

D1Rat24 (e-PCR), detects polymorphism
- UniSTS:118569

RH130271 (e-PCR)
- UniSTS:213558

PMC19579P1 (e-PCR)
- UniSTS:144050

Npas1 (e-PCR), detects polymorphism
- UniSTS:144050

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within maternal behavior	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology 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 startle response	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: neuronal PAS domain-containing protein 1

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_001107479.1 → NP_001100949.1 neuronal PAS domain-containing protein 1

See identical proteins and their annotated locations for NP_001100949.1

Status: PROVISIONAL

Source sequence(s)

CH473979

UniProtKB/TrEMBL

A6J8B4, D3ZJ66

Related

ENSRNOP00000020855.3, ENSRNOT00000020855.6

Conserved Domains (3) summary

smart00091
Location:141 → 198

PAS; PAS domain

pfam08447
Location:317 → 388

PAS_3; PAS fold

cd19731
Location:43 → 116

bHLH-PAS_NPAS1_PASD5; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 1 (NPAS1) and similar proteins

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

86295509..86316018 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006228413.3 → XP_006228475.1 neuronal PAS domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_006228475.1

UniProtKB/TrEMBL

A6J8B4, D3ZJ66

Conserved Domains (3) summary

smart00091
Location:141 → 198

PAS; PAS domain

pfam08447
Location:317 → 388

PAS_3; PAS fold

cd19731
Location:43 → 116

bHLH-PAS_NPAS1_PASD5; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 1 (NPAS1) and similar proteins