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    Npas3 neuronal PAS domain protein 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 299016, updated on 27-Nov-2024

    Summary

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    Symbol
    Npas3provided by RGD
    Full Name
    neuronal PAS domain protein 3provided by RGD
    Primary source
    RGD:1307181
    See related
    EnsemblRapid:ENSRNOG00000068162 AllianceGenome:RGD:1307181
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable protein heterodimerization activity. Predicted to be involved in positive regulation of DNA-templated transcription. Predicted to act upstream of or within locomotory behavior; maternal behavior; and startle response. Predicted to be located in nucleoplasm. Orthologous to human NPAS3 (neuronal PAS domain protein 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 26.4), Kidney (RPKM 3.8) and 2 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Npas3 in Genome Data Viewer
    Location:
    6q23
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (76438064..77263185)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (70702773..71527928)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (74081995..74913025)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene A-kinase anchoring protein 6 Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC102547735 Neighboring gene small nucleolar RNA SNORA2/SNORA34 family Neighboring gene transfer RNA alanine (anticodon AGC) 62 Neighboring gene egl-9 family hypoxia-inducible factor 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Lower NPAS3 expression during the later stages of abnormal lung development in rat congenital diaphragmatic hernia. Pereira-Terra P, et al. Pediatr Surg Int, 2015 Jul. PMID 25862168
    2. Behavioral and regulatory abnormalities in mice deficient in the NPAS1 and NPAS3 transcription factors. Erbel-Sieler C, et al. Proc Natl Acad Sci U S A, 2004 Sep 14. PMID 15347806, Free PMC Article
    3. Scleraxis: a basic helix-loop-helix protein that prefigures skeletal formation during mouse embryogenesis. Cserjesi P, et al. Development, 1995 Apr. PMID 7743923
    4. NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors. Wu D, et al. Elife, 2016 Oct 26. PMID 27782878, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    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 locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within maternal behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription 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 nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    neuronal PAS domain-containing protein 3

    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)

    1. NM_001427296.1 → NP_001414225.1  neuronal PAS domain-containing protein 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000006

    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

    1. NC_086024.1 Reference GRCr8

      Range
      76438064..77263185
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039078152.2 → XP_038934080.1  neuronal PAS domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Conserved Domains (4) summary
      smart00091
      Location:205 → 263
      PAS; PAS domain
      pfam08447
      Location:396 → 483
      PAS_3; PAS fold
      cd19732
      Location:84 → 160
      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:523 → 731
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    2. XM_039078154.2 → XP_038934082.1  neuronal PAS domain-containing protein 3 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Conserved Domains (4) summary
      smart00091
      Location:205 → 263
      PAS; PAS domain
      pfam08447
      Location:396 → 483
      PAS_3; PAS fold
      cd19732
      Location:84 → 160
      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:523 → 645
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    3. XM_039078153.2 → XP_038934081.1  neuronal PAS domain-containing protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Conserved Domains (4) summary
      smart00091
      Location:203 → 261
      PAS; PAS domain
      pfam08447
      Location:394 → 481
      PAS_3; PAS fold
      cd19732
      Location:84 → 160
      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:521 → 729
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    4. XM_039078160.2 → XP_038934088.1  neuronal PAS domain-containing protein 3 isoform X8

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Conserved Domains (4) summary
      smart00091
      Location:175 → 233
      PAS; PAS domain
      pfam08447
      Location:366 → 453
      PAS_3; PAS fold
      cd19732
      Location:53 → 130
      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:493 → 701
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    5. XM_039078155.2 → XP_038934083.1  neuronal PAS domain-containing protein 3 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Related
      ENSRNOP00000096867.2, ENSRNOT00000115753.2
      Conserved Domains (4) summary
      smart00091
      Location:203 → 261
      PAS; PAS domain
      pfam08447
      Location:394 → 481
      PAS_3; PAS fold
      cd19732
      Location:84 → 160
      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:521 → 643
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    6. XM_039078157.2 → XP_038934085.1  neuronal PAS domain-containing protein 3 isoform X6

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Conserved Domains (4) summary
      smart00091
      Location:186 → 244
      PAS; PAS domain
      pfam08447
      Location:377 → 464
      PAS_3; PAS fold
      cd19732
      Location:84 → 160
      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:504 → 712
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    7. XM_039078162.2 → XP_038934090.1  neuronal PAS domain-containing protein 3 isoform X11

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Conserved Domains (4) summary
      smart00091
      Location:156 → 214
      PAS; PAS domain
      pfam08447
      Location:347 → 434
      PAS_3; PAS fold
      cd19732
      Location:53 → 130
      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:474 → 682
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    8. XM_039078156.2 → XP_038934084.1  neuronal PAS domain-containing protein 3 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Conserved Domains (4) summary
      smart00091
      Location:188 → 246
      PAS; PAS domain
      pfam08447
      Location:379 → 466
      PAS_3; PAS fold
      cd19732
      Location:84 → 160
      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:506 → 714
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    9. XM_039078158.2 → XP_038934086.1  neuronal PAS domain-containing protein 3 isoform X7

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Related
      ENSRNOP00000108681.1, ENSRNOT00000166002.1
      Conserved Domains (4) summary
      smart00091
      Location:188 → 246
      PAS; PAS domain
      pfam08447
      Location:379 → 466
      PAS_3; PAS fold
      cd19732
      Location:84 → 160
      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:506 → 628
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    10. XM_063261674.1 → XP_063117744.1  neuronal PAS domain-containing protein 3 isoform X10

      Related
      ENSRNOP00000096479.2, ENSRNOT00000109465.2

    11. XM_039078163.2 → XP_038934091.1  neuronal PAS domain-containing protein 3 isoform X12

      UniProtKB/TrEMBL
      A0A8I6AMQ0, A0A8I6AR06
      Related
      ENSRNOP00000099955.1, ENSRNOT00000173624.1
      Conserved Domains (4) summary
      smart00091
      Location:158 → 216
      PAS; PAS domain
      pfam08447
      Location:349 → 436
      PAS_3; PAS fold
      cd19732
      Location:53 → 130
      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:476 → 598
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    12. XM_039078165.2 → XP_038934093.1  neuronal PAS domain-containing protein 3 isoform X14

      UniProtKB/TrEMBL
      A0A8I6AMQ0, A0A8I6APE0
      Conserved Domains (4) summary
      smart00091
      Location:139 → 197
      PAS; PAS domain
      pfam08447
      Location:330 → 417
      PAS_3; PAS fold
      cd19732
      Location:17 → 94
      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:457 → 665
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    13. XM_063261675.1 → XP_063117745.1  neuronal PAS domain-containing protein 3 isoform X15

      Related
      ENSRNOP00000112538.1, ENSRNOT00000152609.1

    14. XM_039078161.2 → XP_038934089.1  neuronal PAS domain-containing protein 3 isoform X9

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Related
      ENSRNOP00000104570.1, ENSRNOT00000166789.1
      Conserved Domains (4) summary
      smart00091
      Location:169 → 227
      PAS; PAS domain
      pfam08447
      Location:360 → 447
      PAS_3; PAS fold
      cd19732
      Location:48 → 124
      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:487 → 695
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    15. XM_039078164.2 → XP_038934092.1  neuronal PAS domain-containing protein 3 isoform X13

      UniProtKB/TrEMBL
      A0A8I6AMQ0
      Conserved Domains (4) summary
      smart00091
      Location:153 → 211
      PAS; PAS domain
      pfam08447
      Location:344 → 431
      PAS_3; PAS fold
      cd19732
      Location:32 → 108
      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:471 → 679
      MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001106727.1: Suppressed sequence

      Description
      NM_001106727.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: NPAS3 (GeneID:64067).
    Nucleotide Protein Strain
    Heading Accession and Version

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