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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000071813 Accession number: AF152509 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Similar to Protocadherin gamma-A3 isoform 2 precursor.
 
 

Transcript original information
Accession number AF152509.1
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 (PCDHGA3) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGA3);
Sequence data provider NA
Annotation project NA
Length of cDNA 2712[bp] (No. of exon:5)[A:637 T:545 G:730 C:800]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type NA
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature N-truncated
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGAAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0005252
Genomic location  G-integra Help Chromosome 5
Location 5q31.3
Position 140723601- 140890750
Strand +
Possible duplicated location(s) NA
Gene structure 5 exon(s)
Database links RefSeq NM_002588;  NM_003735;  NM_003736;  NM_014004;  NM_018912;  NM_018913;  NM_018914;  NM_018915;  NM_018916;  NM_018917;  NM_018918;  NM_018919;  NM_018920;  NM_018921;  NM_018922;  NM_018923;  NM_018924;  NM_018925;  NM_018926;  NM_018927;  NM_018928;  NM_018929;  NM_031993;  NM_032009;  NM_032011;  NM_032053;  NM_032054;  NM_032086;  NM_032087;  NM_032088;  NM_032089;  NM_032090;  NM_032091;  NM_032092;  NM_032094;  NM_032095;  NM_032096;  NM_032097;  NM_032098;  NM_032099;  NM_032100;  NM_032101;  NM_032402;  NM_032403;  NM_032406;  NM_032407; 
Ensembl ENST00000252085;  ENST00000252087;  ENST00000253812;  ENST00000305759;  ENST00000306593;  ENST00000308177;  ENST00000378105;  ENST00000394576;  ENST00000398587;  ENST00000398594;  ENST00000398604;  ENST00000398610;  ENST00000517417;  ENST00000517434;  ENST00000518069;  ENST00000518325;  ENST00000518882;  ENST00000520790;  ENST00000522605;  ENST00000523390;  ENST00000528330; 
Entrez Gene Entrez Gene ID:56112; 
KEGG GENES KEGG GENES(56112); 
GeneCard GeneCardPCDHGA3;  *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 HIP000183290
Predicted CDS 213..2702;  829[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.773

Motif information
ORF

length(829),orf(213:2702) DAAFLSESAKRQLGHRGEDRPGGALRSDPAVSEELEIKIGELTVPGTRFP IKTAFDPDVGINSLQNYKLSPNDYFSLAVNSVSEGAKYPELVLERALDRE KKEIHQLVLVASDGGDPVHSGNLHIQVIVLDANDNPPMFTQPEYRVSVWE NVPVGTRLLTVNATDPDEGFNAQVSYILDKMPGKIAEIFHLNSVSGEVSI LKSLDYEDAMFYEIKIEAQDGPGLLSRANILVTVLDVNDNAPEITITSLT SSVPEEGTVGREIALIDVHDRDSGQNGQVEVFVLGNLPFKLEKSIDQYYR LVTATSLDREQISEYNISLRASDGGSPPLSTETHITLHVIDINDNPPTFP HLSYSAYIPENNPRGASIFSVTAQDPDSNNNARITYALTEDTLQGAPLSS FVSINSNTGVLYALRSFDYEQFRDLKLLVTASDSGNPPLSSIVSLNLFVL DQNDNAPEILYPALPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAW LSYRLLKASEPGLFSVGLHTGEVRTARALLDRDALKQSLVVAVQDHGQPP LSATVTLTVAVADRIPDILADLGSLEPSAKPNDSDLTLYLVVAVAAVSCV FLAFVIVLLALRLRRWHKSRLLQASGGGLASTPGSHFVGVDGVRAFLQTY SHEVSLTADSRKSHLIFPQPNYADTLISQESCEKSEPLLITQDLLEMKGD SNLLQQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMIL ASASEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNAT LTNAAGKRDGKAPAGGNGNKKKSGKKEKK* 		a.a.
length		 InterPro Name
length(109), motif(31:139) 109 IPR002126 Cadherin [Domain]
length(798), motif(32:829) 798 IPR015492 Protocadherin gamma [Family]
length(100), motif(33:132) 100 IPR015919 Cadherin-like [Domain]
length(104), motif(33:136) 104 IPR002126 Cadherin [Domain]
length(86), motif(52:137) 86 IPR002126 Cadherin [Domain]
length(11), motif(127:137) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(132:236) 105 IPR015919 Cadherin-like [Domain]
length(104), motif(137:240) 104 IPR002126 Cadherin [Domain]
length(30), motif(139:168) 30 IPR002126 Cadherin [Domain]
length(105), motif(140:244) 105 IPR002126 Cadherin [Domain]
length(92), motif(144:235) 92 IPR002126 Cadherin [Domain]
length(82), motif(161:242) 82 IPR002126 Cadherin [Domain]
length(13), motif(211:223) 13 IPR002126 Cadherin [Domain]
length(20), motif(223:242) 20 IPR002126 Cadherin [Domain]
length(11), motif(232:242) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(237:341) 105 IPR015919 Cadherin-like [Domain]
length(105), motif(241:345) 105 IPR002126 Cadherin [Domain]
length(105), motif(245:349) 105 IPR002126 Cadherin [Domain]
length(88), motif(252:339) 88 IPR002126 Cadherin [Domain]
length(82), motif(266:347) 82 IPR002126 Cadherin [Domain]
length(11), motif(337:347) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(110), motif(342:451) 110 IPR015919 Cadherin-like [Domain]
length(114), motif(346:459) 114 IPR002126 Cadherin [Domain]
length(14), motif(347:360) 14 IPR002126 Cadherin [Domain]
length(110), motif(350:459) 110 IPR002126 Cadherin [Domain]
length(96), motif(354:449) 96 IPR002126 Cadherin [Domain]
length(87), motif(371:457) 87 IPR002126 Cadherin [Domain]
length(27), motif(407:433) 27 IPR002126 Cadherin [Domain]
length(18), motif(441:458) 18 IPR002126 Cadherin [Domain]
length(11), motif(447:457) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(112), motif(452:563) 112 IPR015919 Cadherin-like [Domain]
length(104), motif(476:579) 104 IPR002126 Cadherin [Domain]
length(88), motif(476:563) 88 IPR002126 Cadherin [Domain]
length(83), motif(479:561) 83 IPR002126 Cadherin [Domain]
length(79), motif(488:566) 79 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000071813
H-Inv cluster ID Locus viewHIX0005252
Accession number AF152509.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Similar to Protocadherin gamma-A3 isoform 2 precursor.
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (NP_114400)  [Identity/coverage = 99.613%/97.47%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
Gene family/group Gene family H-Inv gene family/group ID HIF0000005
Gene family/group name Putative Zinc finger, C2H2-type (IPR007087).
Evidence motif (InterPro) ID IPR007087
Gene symbol/name HGNC symbol PCDHGA3
HGNC aliases NA
HGNC name protocadherin gamma subfamily A, 3
DDBJ NA
UniProt NA
EC number NA
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 HIP000183290
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NM_002588;  NM_003735;  NM_003736;  NM_014004;  NM_018912;  NM_018913;  NM_018914;  NM_018915;  NM_018916;  NM_018917;  NM_018918;  NM_018919;  NM_018920;  NM_018921;  NM_018922;  NM_018923;  NM_018924;  NM_018925;  NM_018926;  NM_018927;  NM_018928;  NM_018929;  NM_031993;  NM_032009;  NM_032011;  NM_032053;  NM_032054;  NM_032086;  NM_032087;  NM_032088;  NM_032089;  NM_032090;  NM_032091;  NM_032092;  NM_032094;  NM_032095;  NM_032096;  NM_032097;  NM_032098;  NM_032099;  NM_032100;  NM_032101;  NM_032402;  NM_032403;  NM_032406;  NM_032407; 
Ensembl ENST00000252085;  ENST00000252087;  ENST00000253812;  ENST00000305759;  ENST00000306593;  ENST00000308177;  ENST00000378105;  ENST00000394576;  ENST00000398587;  ENST00000398594;  ENST00000398604;  ENST00000398610;  ENST00000517417;  ENST00000517434;  ENST00000518069;  ENST00000518325;  ENST00000518882;  ENST00000520790;  ENST00000522605;  ENST00000523390;  ENST00000528330; 
Entrez Gene Entrez Gene ID:56112; 
KEGG GENES KEGG GENES(56112); 
GeneCard GeneCardPCDHGA3;  *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases; 
Curation status Auto-annotated
Notes NA
Related H-InvDB links Putative Zinc finger, C2H2-type (IPR007087). 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 calcium ion binding (GO:0005509); 
Biological process homophilic cell adhesion (GO:0007156); 
Cellular component membrane (GO:0016020); 

Subcellular localization information  Last modified:20-Apr-2012
WoLF PSORT cytosol;  mitochondria;  nuclear;  Other; 
Target P Other
SOSUI membrane protein
TMHMM membrane 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
2 284 2nlzA1 2e-53 12.6 261/533 d.153.1.6
344 427 1edhA1 4e-14 14.6 83/99 b.1.6.1
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 AGhsA110121; 
Affymetrix
GeneChip		 HG-Focus 211875_x_at;  216343_at; 
HG-U133 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at;  216352_x_at; 
HG-U133A 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at;  216352_x_at; 
HG-U133A_2 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at;  216352_x_at; 
HG-U133B NA
HG-U133_Plus_2 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at;  216352_x_at; 
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832553;  2832555;  2832751;  2832754;  2832758;  2832759;  2832760;  2832761;  2878647;  2878651; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_23_P422044;  A_24_P334529; 
Related H-InvDB links H-ANGELH-ANGEL;  DNAProbeLocatorDNAProbeLocator; 

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:20-Apr-2012
Disease relation Disease name:NA
Related information in OMIM OMIM ID:NA Title:NA
Co-localized orphan diseases OMIM ID:  601888;  608850;  611091;  612554;  612571; 
Disease related mutation NA
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(56112)
Disease Entrez Gene ID:(56112)
Substance Entrez Gene ID:(56112)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo Viewer;  LEGENDALEGENDA; 

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
13 .. 13 C/T rs76843294 + 5'UTR
118 .. 118 G/C rs76939403 + 5'UTR
185 .. 185 G/A rs114467342 + 5'UTR
235 .. 235 C/T rs11575947 + CDS Nonsynonymous[Ser8Phe]
363 .. 363 A/C rs11575948 + CDS Nonsynonymous[Ile51Leu]
464 .. 464 G/A rs112672535 + CDS Synonymous[Glu84Glu]
894 .. 894 G/T rs72790006 + CDS Nonsynonymous[Ala228Ser]
1199 .. 1199 G/C rs7730183 + CDS Synonymous[Leu329Leu]
1544 .. 1544 G/T rs2879225 + CDS Synonymous[Ser444Ser]
1553 .. 1553 G/A rs2879226 + CDS Synonymous[Leu447Leu]
1557 .. 1557 G/C rs2879227 + CDS Nonsynonymous[Val449Leu]
1640 .. 1640 T/C rs3749774 - CDS Synonymous[Pro476Pro]
1642 .. 1642 G/T rs4042102 + CDS Nonsynonymous[Arg477Leu]
1782 .. 1782 C/A rs62378406 + CDS Nonsynonymous[Arg524Ser]
1826 .. 1826 C/T rs112486508 + CDS Synonymous[Ser538Ser]
1826 .. 1826 C/T rs7736087 + CDS Synonymous[Ser538Ser]
1839 .. 1839 G/A rs61749030 + CDS Nonsynonymous[Val543Ile]
1862 .. 1862 T/G rs112347072 + CDS Synonymous[Pro550Pro]
2111 ^ 2112 -/G rs35104607 + CDS
2131 .. 2131 T/C rs7736541 + CDS Nonsynonymous[Val640Ala]
2161 .. 2161 A/G rs10069396 + CDS Nonsynonymous[Tyr650Cys]
2532 .. 2532 G/A rs114669158 + CDS Nonsynonymous[Ala774Thr]
2543 .. 2543 A/G rs2233612 + CDS Synonymous[Gly777Gly]
2565 .. 2565 G/A rs116366286 + CDS Nonsynonymous[Val785Met]
2578 .. 2578 G/A rs61749029 + CDS Nonsynonymous[Arg789His]
 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;