U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 29512, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    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, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 13.2), Spleen (RPKM 7.2) and 8 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    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 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 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

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

      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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous