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Padi4 peptidyl arginine deiminase 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 29512, updated on 4-Jan-2025

Summary

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Official Symbol
Padi4provided by RGD
Official Full Name
peptidyl arginine deiminase 4provided by RGD
Primary source
RGD:3290
See related
EnsemblRapid:ENSRNOG00000006855 AllianceGenome:RGD:3290
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
Pdi4
Summary
Enables protein-arginine deiminase activity. Predicted to be involved in nucleosome assembly; post-translational protein modification; and stem cell population maintenance. Predicted to be part of protein-containing complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human PADI4 (peptidyl arginine deiminase 4). [provided by Alliance of Genome Resources, Jan 2025]
Expression
Biased expression in Lung (RPKM 13.2), Spleen (RPKM 7.2) and 8 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Padi4 in Genome Data Viewer
Location:
5q36
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (158324417..158357466, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (153041351..153074412, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (159260675..159293906, complement)

Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene regulator of chromosome condensation 2 Neighboring gene small nucleolar RNA SNORA15 Neighboring gene peptidyl arginine deiminase 6 Neighboring gene peptidyl arginine deiminase 3 Neighboring gene peptidyl arginine deiminase 1 Neighboring gene transfer RNA alanine (anticodon GGC) 1

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. Cloning of cDNA encoding a novel isoform (type IV) of peptidylarginine deiminase from rat epidermis. Yamakoshi A, et al. Biochim Biophys Acta, 1998 Jul 28. PMID 9675292
  2. Citrullination regulates pluripotency and histone H1 binding to chromatin. Christophorou MA, et al. Nature, 2014 Mar 6. PMID 24463520, Free PMC Article
  3. Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4. Arita K, et al. Proc Natl Acad Sci U S A, 2006 Apr 4. PMID 16567635, Free PMC Article
  4. Structural basis for Ca(2+)-induced activation of human PAD4. Arita K, et al. Nat Struct Mol Biol, 2004 Aug. PMID 15247907
  5. Molecular cloning of two novel types of peptidylarginine deiminase cDNAs from retinoic acid-treated culture of a newborn rat keratinocyte cell line. Ishigami A, et al. FEBS Lett, 1998 Aug 14. PMID 9738944

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables calcium ion binding ISO
Inferred from Sequence Orthology
more info
  
enables calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H1R54 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H2AR3 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3R17 arginine deiminase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3R2 arginine deiminase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3R26 arginine deiminase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3R8 arginine deiminase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H4R3 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone arginine deiminase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone arginine deiminase activity ISO
Inferred from Sequence Orthology
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables protein-arginine deiminase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein-arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein-arginine deiminase activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in chromatin organization ISO
Inferred from Sequence Orthology
more info
  
involved_in chromatin organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
involved_in chromatin remodeling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleosome assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in nucleosome assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in post-translational protein modification ISO
Inferred from Sequence Orthology
more info
  
involved_in stem cell population maintenance ISO
Inferred from Sequence Orthology
more info
  
involved_in stem cell population maintenance ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
protein-arginine deiminase type-4
Names
PAD-R4
peptidyl arginine deiminase, type 4
peptidyl arginine deiminase, type IV
peptidylarginine deiminase IV
peptidylarginine deiminase type alpha
protein-arginine deiminase type IV
NP_058923.1
XP_006239207.3
XP_017448694.1
XP_017448695.1

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)

  1. NM_017227.1 → NP_058923.1  protein-arginine deiminase type-4

    See identical proteins and their annotated locations for NP_058923.1

    Status: PROVISIONAL

    Source sequence(s)
    AB010999
    UniProtKB/Swiss-Prot
    O35117, O88807
    UniProtKB/TrEMBL
    A0A8I6ADU5, A6ITP3
    Related
    ENSRNOP00000009081.2, ENSRNOT00000009081.4
    Conserved Domains (3) summary
    pfam03068
    Location:286 → 663
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 111
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:113 → 272
    PAD_M; Protein-arginine deiminase (PAD) middle domain

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
    158324417..158357466 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006239145.5 → XP_006239207.3  protein-arginine deiminase type-4 isoform X3

    UniProtKB/TrEMBL
    A0A8I6ADU5
    Related
    ENSRNOP00000100592.1, ENSRNOT00000133152.1

  2. XM_017593206.3 → XP_017448695.1  protein-arginine deiminase type-4 isoform X2

    UniProtKB/TrEMBL
    A0A8I6ADU5
    Related
    ENSRNOP00000099571.1, ENSRNOT00000132511.1

  3. XM_017593205.3 → XP_017448694.1  protein-arginine deiminase type-4 isoform X1

    UniProtKB/TrEMBL
    A0A8I6ADU5
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O88807.1 GenPept UniProtKB/Swiss-Prot:O88807

Gene LinkOut

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