H-InvDB x AHG DB
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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000058537 Accession number: AB017919 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Protein-arginine deiminase type-4; EC=3.5.3.15; HL-60 PAD; Peptidylarginine deiminase IV; Protein-arginine deiminase type IV;
 
 

Transcript original information
Accession number AB017919.1
CAGE tag ID NA
EST ID NA
Clone Number NA
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PADI4) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PADI4);
Sequence data provider NA
Annotation project NA
Length of cDNA 2263[bp] (No. of exon:16)[A:517 T:454 G:622 C:670]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type NA
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGGAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0000182
Genomic location  G-integra Help Chromosome 1
Location 1p36.13
Position 17634692- 17690495
Strand +
Possible duplicated location(s) NA
Gene structure 16 exon(s)
Database links RefSeq NM_012387; 
Ensembl ENST00000358829;  ENST00000375448;  ENST00000375453;  ENST00000467001;  ENST00000468945;  ENST00000487048; 
Entrez Gene Entrez Gene ID:23569; 
KEGG GENES KEGG GENES(23569); 
GeneCard GeneCardPADI4;  *GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS;  G-integraG-integra;  cDNA-genome alignmentcDNA-genome alignment; 

Predicted CDS information
HIP ID HIP000032060
Predicted CDS 27..2018;  663[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.855

Motif information
ORF

length(663),orf(27:2018) MAQGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVV DIAHSPPAKKKSTGSSTWPLDPGVEVTLTMKAASGSTGDQKVQISYYGPK TPPVKALLYLTAVEISLCADITRTGKVKPTRAVKDQRTWTWGPCGQGAIL LVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLV LHVARSEMDKVRVFQATRGKLSSKCSVVLGPKWPSHYLMVPGGKHNMDFY VEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTP NTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTICPEEENMDDQWMQD EMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGG ISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDF LSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKL FQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNR ELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPK PFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHCGTNVR RKPFSFKWWNMVP* 		a.a.
length		 InterPro Name
length(663), motif(1:663) 663 IPR016296 Protein-arginine deiminase, subgroup [Family]
length(111), motif(1:111) 111 IPR013732 Protein-arginine deiminase (PAD) N-terminal [Domain]
length(660), motif(2:661) 660 IPR004303 Protein-arginine deiminase [Family]
length(109), motif(4:112) 109 IPR008972 Cupredoxin [Domain]
length(181), motif(113:293) 181 IPR013733 Protein-arginine deiminase (PAD), central domain [Domain]
length(161), motif(113:273) 161 IPR013733 Protein-arginine deiminase (PAD), central domain [Domain]
length(386), motif(278:663) 386 IPR013530 Protein-arginine deiminase, C-terminal [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000058537
H-Inv cluster ID Locus viewHIX0000182
Accession number AB017919.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protein-arginine deiminase type-4; EC=3.5.3.15; HL-60 PAD; Peptidylarginine deiminase IV; Protein-arginine deiminase type IV;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q9UM07)  [Identity/coverage = 99.397%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 10488123;  11435484;  12833157;  15087120;  15247907;  15338034;  15339660;  15345777;  15489334;  15629448;  15731352;  16710414;  ALL; 
Gene family/group Gene family H-Inv gene family/group ID HIF0000651
Gene family/group name Protein-arginine deiminase, subgroup (IPR016296).
Evidence motif (InterPro) ID IPR016296
Gene symbol/name HGNC symbol PADI4
HGNC aliases "peptidyl arginine deiminase, type V"
HGNC name peptidyl arginine deiminase, type IV
DDBJ NA
UniProt PADI4
EC number EC 3.5.3.15protein-arginine deiminase; 
GGDB
(GlycoGene Database)
 Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000032060
No. of interaction 1
Interaction partner(s) HIP000099222; 
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct EBI-3927272; 
Database links RefSeq NM_012387; 
Ensembl ENST00000358829;  ENST00000375448;  ENST00000375453;  ENST00000467001;  ENST00000468945;  ENST00000487048; 
Entrez Gene Entrez Gene ID:23569; 
KEGG GENES KEGG GENES(23569); 
GeneCard GeneCardPADI4;  *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases; 
Curation status Human curated
Notes NA
Related H-InvDB links Protein-arginine deiminase, subgroup (IPR016296). Similarity Search ToolSimilarity Search Tool;  TACTTACT; 
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA

Gene ontology information
Molecular function protein-arginine deiminase activity (GO:0004668);  calcium ion binding (GO:0005509); 
Biological process protein modification process (GO:0006464);  peptidyl-citrulline biosynthetic process from peptidyl-arginine (GO:0018101); 
Cellular component cytoplasm (GO:0005737); 

Subcellular localization information  Last modified:20-Apr-2012
WoLF PSORT extracellular;  cytosol;  nuclear;  Other; 
Target P Other
SOSUI soluble protein
TMHMM soluble protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP) GTOP Last modified:20-Apr-2012
Start End PDB_ID E-value Identity Coverage SCOP_ID
4 112 1wd8A2 1e-34 97.8 92/92 b.6.1.6
113 293 1wd8A1 3e-65 89.7 155/155 b.2.9.1
294 663 1wd8A3 e-166 97.4 310/310 d.126.1.5
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:20-Apr-2012
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator		 AceGene AGhsA010721; 
Affymetrix
GeneChip		 HG-Focus 220001_at; 
HG-U133 211413_s_at;  220001_at; 
HG-U133A 211413_s_at;  220001_at; 
HG-U133A_2 211413_s_at;  220001_at; 
HG-U133B NA
HG-U133_Plus_2 211413_s_at;  220001_at; 
HG-U95 75941_at;  86508_at; 
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D 75941_at;  86508_at; 
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2322849;  2322850;  2322856;  2322857;  2322859;  2322861;  2322863;  2322865;  2322866;  2322867;  2322868;  2322869;  2322877;  2322879;  2322880;  2322882;  2322883;  2322884;  2322885; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P138260; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P138262;  A_23_P369502; 
Related H-InvDB links H-ANGELH-ANGEL;  DNAProbeLocatorDNAProbeLocator; 

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:20-Apr-2012
Disease relation Disease name: {Rheumatoid arthritis, susceptibility to} (180300); 
Related information in OMIM OMIM ID:  605347;  Title: PEPTIDYLARGININE DEIMINASE, TYPE IV
Co-localized orphan diseases OMIM ID:  115665;  116600;  155600;  600975;  605225;  605606;  606788;  606852;  606928;  607317;  607671;  608543;  608553;  608995;  610320;  612367;  612596; 
Disease related mutation MutationView:  605347; 
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(23569)
Disease Entrez Gene ID:(23569)
Substance Entrez Gene ID:(23569)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo Viewer;  LEGENDALEGENDA; 

Evolutionary information  Evola Help Last modified:20-Apr-2012
Relationship Species Accession number MGI Links
Orthology Rattus sp. (Rat) AB010999 G-integraG-integra
Orthology Mus sp. (Mouse) AK137625 MGI:3541041 G-integraG-integra
Orthology Canis sp. (Dog) ENSCAFT00000035689 G-integraG-integra
Orthology Equus sp. (Horse) ENSECAT00000011664 G-integraG-integra
Orthology Monodelphis sp. (Opossum) ENSMODT00000003331 G-integraG-integra
Orthology Oryzias sp. (Medaka) ENSORLT00000009420 G-integraG-integra
Orthology Pongo sp. (Orangutan) ENSPPYT00000002163 G-integraG-integra
Orthology Gallus sp. (Chicken) XM_425729 G-integraG-integra
Orthology Pan sp. (Chimpanzee) XM_513116 G-integraG-integra
Orthology Bos sp. (Cow) XM_584904 G-integraG-integra
Orthology Macaca sp. (Macaque) XR_010782 G-integraG-integra
Phylogenetic tree [View by ATV]
 Neighbor-joining (phb) 
Related H-InvDB links EvolaEvola;  dN/dS (under constraction); 

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
12 .. 12 C/T rs79614405 + 5'UTR
49 .. 49 G/A rs35381732 + CDS Nonsynonymous[Arg8His]
76 .. 76 C/A rs112918821 + CDS Nonsynonymous[Ala17Asp]
189 .. 189 A/G rs11203366 + CDS Nonsynonymous[Ser55Gly]
191 .. 191 C/T rs77182432 + CDS Synonymous[Ser55Ser]
247 .. 247 T/C rs57969340 + CDS Nonsynonymous[Val74Ala]
262 .. 262 C/T rs35809521 + CDS Nonsynonymous[Thr79Met]
271 .. 271 C/T rs11203367 + CDS Nonsynonymous[Ala82Val]
330 .. 330 C/A rs34309058 + CDS Nonsynonymous[Pro102Thr]
361 .. 361 C/G rs874881 + CDS Nonsynonymous[Ala112Gly]
375 .. 375 C/T rs1748033 - CDS Synonymous[Leu117Leu]
418 .. 418 G/C rs12733102 + CDS Nonsynonymous[Arg131Thr]
461 .. 461 A/G rs79899387 + CDS Synonymous[Gly145Gly]
517 .. 517 T/C rs11588132 + CDS Nonsynonymous[Met164Thr]
524 .. 524 C/T rs111275753 + CDS Synonymous[Cys166Cys]
749 .. 749 C/T rs16825565 + CDS Synonymous[Pro241Pro]
750 .. 750 G/A rs41265995 + CDS Nonsynonymous[Gly242Ser]
804 .. 804 G/A rs35903413 + CDS Nonsynonymous[Asp260Asn]
811 .. 811 C/T rs34743635 + CDS Nonsynonymous[Pro262Leu]
820 .. 820 T/G rs76133149 + CDS Nonsynonymous[Ile265Ser]
847 .. 847 C/T rs41265997 + CDS Nonsynonymous[Thr274Met]
850 .. 850 C/T rs1748020 - CDS Nonsynonymous[Ser275Phe]
904 .. 904 T/C rs113714693 + CDS Nonsynonymous[Val293Ala]
952 .. 952 A/G rs33981382 + CDS Nonsynonymous[Tyr309Cys]
1115 .. 1115 G/A rs17852287 + CDS Synonymous[Thr363Thr]
1175 .. 1175 A/C rs2240335 - CDS Synonymous[Arg383Arg]
1298 .. 1298 G/A rs35240185 + CDS Synonymous[Pro424Pro]
1553 .. 1553 C/T rs2301887 - CDS Synonymous[His509His]
1862 .. 1862 G/A rs2301886 - CDS Synonymous[Leu612Leu]
2044 .. 2044 C/T rs77757441 + 3'UTR
2144 .. 2144 T/C rs34954650 + 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD); 
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer;