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    Pax5 paired box 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500453, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Pax5provided by RGD
    Official Full Name
    paired box 5provided by RGD
    Primary source
    RGD:1565236
    See related
    EnsemblRapid:ENSRNOG00000024729 AllianceGenome:RGD:1565236
    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
    Also known as
    RGD1565236
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in nervous system development; regulation of transcription by RNA polymerase II; and sensory organ development. Predicted to act upstream of or within several processes, including embryonic cranial skeleton morphogenesis; regulation of transcription by RNA polymerase II; and telencephalon development. Predicted to be located in nucleoplasm. Human ortholog(s) of this gene implicated in acute lymphoblastic leukemia. Orthologous to human PAX5 (paired box 5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward (RPKM 202.2) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pax5 in Genome Data Viewer
    Location:
    5q22
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (63554784..63741380, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (58763334..58945719, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (60007587..60191973, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA17 Neighboring gene heterogeneous nuclear ribonucleoprotein K-like Neighboring gene uncharacterized LOC120102862 Neighboring gene zinc finger CCHC-type containing 7 Neighboring gene uncharacterized LOC134487064

    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 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. GABAergic neurons regulate lateral ventricular development via transcription factor Pax5. Ohtsuka N, et al. Genesis, 2013 Apr. PMID 23349049, Free PMC Article
    2. B cell-specific loss of histone 3 lysine 9 methylation in the V(H) locus depends on Pax5. Johnson K, et al. Nat Immunol, 2004 Aug. PMID 15258579, Free PMC Article
    3. Repression of Flt3 by Pax5 is crucial for B-cell lineage commitment. Holmes ML, et al. Genes Dev, 2006 Apr 15. PMID 16618805, Free PMC Article
    4. Lymphoid enhancer-binding factor-1 binds and activates the recombination-activating gene-2 promoter together with c-Myb and Pax-5 in immature B cells. Jin ZX, et al. J Immunol, 2002 Oct 1. PMID 12244173
    5. Activation of mouse RAG-2 promoter by Myc-associated zinc finger protein. Wu CX, et al. Biochem Biophys Res Commun, 2004 May 14. PMID 15094381

    See all (8) citations in PubMed

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within adult behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cerebral cortex development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within embryonic cranial skeleton morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lateral ventricle development 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 nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within 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
    		  
    involved_in sensory organ development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within skeletal muscle cell differentiation 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
    paired box protein Pax-5

    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_001109261.1 → NP_001102731.1  paired box protein Pax-5

      See identical proteins and their annotated locations for NP_001102731.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473962
      UniProtKB/TrEMBL
      A0A8I5ZL27, A6IJ74, F1M4W2
      Related
      ENSRNOP00000078511.1, ENSRNOT00000117108.2
      Conserved Domains (2) summary
      smart00351
      Location:16 → 140
      PAX; Paired Box domain
      pfam12403
      Location:279 → 389
      Pax2_C; Paired-box protein 2 C terminal

    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_086023.1 Reference GRCr8

      Range
      63554784..63741380 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039110570.2 → XP_038966498.1  paired box protein Pax-5 isoform X4

      Conserved Domains (2) summary
      pfam12403
      Location:190 → 300
      Pax2_C; Paired-box protein 2 C terminal
      cl21459
      Location:1 → 34
      HTH; Helix-turn-helix domains

    2. XM_039110568.2 → XP_038966496.1  paired box protein Pax-5 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AHR4, F1M4W2
      Related
      ENSRNOP00000087974.1, ENSRNOT00000112306.2
      Conserved Domains (2) summary
      smart00351
      Location:16 → 140
      PAX; Paired Box domain
      pfam12403
      Location:236 → 346
      Pax2_C; Paired-box protein 2 C terminal

    3. XM_039110567.2 → XP_038966495.1  paired box protein Pax-5 isoform X2

      UniProtKB/TrEMBL
      F1M4W2
      Conserved Domains (2) summary
      smart00351
      Location:16 → 140
      PAX; Paired Box domain
      pfam12403
      Location:255 → 365
      Pax2_C; Paired-box protein 2 C terminal

    4. XM_039110563.2 → XP_038966491.1  paired box protein Pax-5 isoform X1

      UniProtKB/TrEMBL
      F1M4W2
      Related
      ENSRNOP00000108398.1, ENSRNOT00000144309.1
      Conserved Domains (2) summary
      smart00351
      Location:16 → 140
      PAX; Paired Box domain
      pfam12403
      Location:298 → 408
      Pax2_C; Paired-box protein 2 C terminal

    5. XM_039110569.2 → XP_038966497.1  paired box protein Pax-5 isoform X4

      Conserved Domains (2) summary
      pfam12403
      Location:190 → 300
      Pax2_C; Paired-box protein 2 C terminal
      cl21459
      Location:1 → 34
      HTH; Helix-turn-helix domains
    Nucleotide Protein Strain
    Heading Accession and Version

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