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Pcbp3 poly(rC) binding protein 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 294336, updated on 2-Nov-2024

Summary

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Official Symbol
Pcbp3provided by RGD
Official Full Name
poly(rC) binding protein 3provided by RGD
Primary source
RGD:1307430
See related
EnsemblRapid:ENSRNOG00000001245 AllianceGenome:RGD:1307430
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 C-rich single-stranded DNA binding activity and mRNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be active in cytoplasm and nucleus. Orthologous to human PCBP3 (poly(rC) binding protein 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Testes (RPKM 84.0), Thymus (RPKM 62.1) and 7 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Pcbp3 in Genome Data Viewer
Location:
20p12
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (11635579..11877721)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (11678218..11878210)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (12429255..12629985)

Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene collagen type XVIII alpha 1 chain Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 4, pseudogene 5 Neighboring gene solute carrier family 19 member 1 Neighboring gene adenosylhomocysteinase, pseudogene 1 Neighboring gene uncharacterized LOC120098922 Neighboring gene collagen type VI alpha 1 chain

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. Novel dual-binding function of a poly (C)-binding protein 3, transcriptional factor which binds the double-strand and single-stranded DNA sequence. Kang DH, et al. Gene, 2012 Jun 10. PMID 22521865
  2. Regulators of Iron Homeostasis: New Players in Metabolism, Cell Death, and Disease. Bogdan AR, et al. Trends Biochem Sci, 2016 Mar. PMID 26725301, Free PMC Article
  3. Cellular iron uptake, trafficking and metabolism: Key molecules and mechanisms and their roles in disease. Lane DJ, et al. Biochim Biophys Acta, 2015 May. PMID 25661197
  4. Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins. Hu YH, et al. BMC Genomics, 2006 Jun 16. PMID 16780588, Free PMC Article
  5. In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine. Principe S, et al. Proteomics, 2013 May. PMID 23533145, Free PMC Article

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 C-rich single-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
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
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
poly(rC)-binding 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_001011945.2 → NP_001011945.2  poly(rC)-binding protein 3

    Status: VALIDATED

    Source sequence(s)
    BC079196, JAXUCZ010000020
    UniProtKB/TrEMBL
    F7F4P9
    Conserved Domains (3) summary
    cd22516
    Location:38 → 114
    KH-I_PCBP3_rpt1; first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22522
    Location:266 → 340
    KH-I_PCBP3_rpt3; third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) 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

  1. NC_086038.1 Reference GRCr8

    Range
    11635579..11877721
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063279058.1 → XP_063135128.1  poly(rC)-binding protein 3 isoform X5

    UniProtKB/TrEMBL
    A6JKB2
    Related
    ENSRNOP00000077332.2, ENSRNOT00000104059.2

  2. XM_039098578.2 → XP_038954506.1  poly(rC)-binding protein 3 isoform X6

    UniProtKB/TrEMBL
    A0A8I5Y0N5
    Conserved Domains (3) summary
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22522
    Location:285 → 359
    KH-I_PCBP3_rpt3; third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cl00098
    Location:38 → 114
    KH-I; K homology (KH) RNA-binding domain, type I

  3. XM_039098577.2 → XP_038954505.1  poly(rC)-binding protein 3 isoform X5

    UniProtKB/TrEMBL
    A0A8I5Y0N5, A6JKB2
    Related
    ENSRNOP00000102769.1, ENSRNOT00000159135.1
    Conserved Domains (3) summary
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22522
    Location:286 → 360
    KH-I_PCBP3_rpt3; third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cl00098
    Location:38 → 114
    KH-I; K homology (KH) RNA-binding domain, type I

  4. XM_039098572.2 → XP_038954500.1  poly(rC)-binding protein 3 isoform X2

    UniProtKB/TrEMBL
    A0A8I5Y0N5
    Conserved Domains (4) summary
    pfam03154
    Location:181 → 314
    Atrophin-1; Atrophin-1 family
    cd22516
    Location:38 → 114
    KH-I_PCBP3_rpt1; first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22522
    Location:308 → 382
    KH-I_PCBP3_rpt3; third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins

  5. XM_006256283.5 → XP_006256345.1  poly(rC)-binding protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006256345.1

    UniProtKB/TrEMBL
    A0A8I5Y0N5
    Conserved Domains (4) summary
    pfam03154
    Location:181 → 315
    Atrophin-1; Atrophin-1 family
    cd22516
    Location:38 → 114
    KH-I_PCBP3_rpt1; first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22522
    Location:309 → 383
    KH-I_PCBP3_rpt3; third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins

  6. XM_039098575.2 → XP_038954503.1  poly(rC)-binding protein 3 isoform X3

    UniProtKB/TrEMBL
    F7F4P9
    Related
    ENSRNOP00000001675.6, ENSRNOT00000001675.6
    Conserved Domains (3) summary
    cd22516
    Location:38 → 114
    KH-I_PCBP3_rpt1; first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22522
    Location:289 → 363
    KH-I_PCBP3_rpt3; third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins

  7. XM_039098576.2 → XP_038954504.1  poly(rC)-binding protein 3 isoform X4

    UniProtKB/TrEMBL
    F7F4P9
    Conserved Domains (4) summary
    pfam03154
    Location:181 → 298
    Atrophin-1; Atrophin-1 family
    cd22516
    Location:38 → 114
    KH-I_PCBP3_rpt1; first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22522
    Location:288 → 362
    KH-I_PCBP3_rpt3; third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins

  8. XM_039098580.2 → XP_038954508.1  poly(rC)-binding protein 3 isoform X9

    UniProtKB/TrEMBL
    F7F4P9
    Conserved Domains (3) summary
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22522
    Location:265 → 339
    KH-I_PCBP3_rpt3; third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cl00098
    Location:38 → 114
    KH-I; K homology (KH) RNA-binding domain, type I

  9. XM_063279064.1 → XP_063135134.1  poly(rC)-binding protein 3 isoform X12

  10. XM_063279065.1 → XP_063135135.1  poly(rC)-binding protein 3 isoform X14

  11. XM_063279062.1 → XP_063135132.1  poly(rC)-binding protein 3 isoform X10

  12. XM_063279063.1 → XP_063135133.1  poly(rC)-binding protein 3 isoform X11

  13. XM_039098583.2 → XP_038954511.1  poly(rC)-binding protein 3 isoform X13

    Conserved Domains (2) summary
    cd22516
    Location:38 → 114
    KH-I_PCBP3_rpt1; first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins

  14. XM_039098585.2 → XP_038954513.1  poly(rC)-binding protein 3 isoform X16

    Conserved Domains (2) summary
    cd22516
    Location:38 → 114
    KH-I_PCBP3_rpt1; first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cd22519
    Location:125 → 203
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins

  15. XM_039098584.2 → XP_038954512.1  poly(rC)-binding protein 3 isoform X15

    Conserved Domains (2) summary
    cd22519
    Location:125 → 202
    KH-I_PCBP3_rpt2; second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins
    cl00098
    Location:38 → 114
    KH-I; K homology (KH) RNA-binding domain, type I

  16. XM_063279056.1 → XP_063135126.1  poly(rC)-binding protein 3 isoform X1

    Related
    ENSRNOP00000076709.2, ENSRNOT00000103785.2

  17. XM_063279057.1 → XP_063135127.1  poly(rC)-binding protein 3 isoform X5

    UniProtKB/TrEMBL
    A6JKB2
    Related
    ENSRNOP00000082318.2, ENSRNOT00000098898.2

  18. XM_063279061.1 → XP_063135131.1  poly(rC)-binding protein 3 isoform X8

  19. XM_063279059.1 → XP_063135129.1  poly(rC)-binding protein 3 isoform X6

  20. XM_063279060.1 → XP_063135130.1  poly(rC)-binding protein 3 isoform X7

RNA

  1. XR_010060648.1 RNA Sequence

  2. XR_005497206.2 RNA Sequence

  3. XR_010060649.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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