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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000252990 Accession number: AY358946 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Protocadherin gamma-A12 isoform 2 precursor.
 
 

Transcript original information
Accession number AY358946.1
CAGE tag ID NA
EST ID NA
Clone Number DNA48306
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PCDHGA12) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGA12);
Sequence data provider NA
Annotation project NA
Length of cDNA 3313[bp] (No. of exon:2)[A:792 T:718 G:890 C:913]
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) NA
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 140809958- 140813405
Strand +
Possible duplicated location(s) NA
Gene structure 2 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:26025; 
KEGG GENES KEGG GENES(26025); 
GeneCard GeneCardPCDHGA12;  *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 HIP000064974
Predicted CDS 371..3121;  916[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.732

Motif information
ORF

length(916),orf(371:3121) MIPARLHRDYKGLVLLGILLGTLWETGCTQIRYSVPEELEKGSRVGDISR DLGLEPRELAERGVRIIPRGRTQLFALNPRSGSLVTAGRIDREELCMGAI KCQLNLDILMEDKVKIYGVEVEVRDINDNAPYFRESELEIKISENAATEM RFPLPHAWDPDIGKNSLQSYELSPNTHFSLIVQNGADGSKYPELVLKRAL DREEKAAHHLVLTASDGGDPVRTGTARIRVMVLDANDNAPAFAQPEYRAS VPENLALGTQLLVVNATDPDEGVNAEVRYSFRYVDDKAAQVFKLDCNSGT ISTIGELDHEESGFYQMEVQAMDNAGYSARAKVLITVLDVNDNAPEVVLT SLASSVPENSPRGTLIALLNVNDQDSEENGQVICFIQGNLPFKLEKSYGN YYSLVTDIVLDREQVPSYNITVTATDRGTPPLSTETHISLNVADTNDNPP VFPQASYSAYIPENNPRGVSLVSVTAHDPDCEENAQITYSLAENTIQGAS LSSYVSINSDTGVLYALSSFDYEQFRDLQVKVMARDNGHPPLSSNVSLSL FVLDQNDNAPEILYPALPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQ NAWLSYRLLKASEPGLFSVGLHTGEVRTARALLDRDALKQSLVVAVQDHG QPPLSATVTLTVAVADSIPQVLADLGSLESPANSETSDLTLYLVVAVAAV SCVFLAFVILLLALRLRRWHKSRLLQASGGGLTGAPASHFVGVDGVQAFL QTYSHEVSLTTDSRKSHLIFPQPNYADMLVSQESFEKSEPLLLSGDSVFS KDSHGLIEVSLYQIFFLFFFNCSVSQAGVQRYDHSSLRPQTPRLKQLSHL CLRCNRDYRCKPPTVCLSIYLSIYLSIYLSIYLLLSCTDGSLTPVIPVLW EAEAGGSPEVGSLRPA* 		a.a.
length		 InterPro Name
length(794), motif(4:797) 794 IPR015492 Protocadherin gamma [Family]
length(97), motif(29:125) 97 IPR015919 Cadherin-like [Domain]
length(83), motif(30:112) 83 IPR013164 Cadherin, N-terminal [Domain]
length(100), motif(30:129) 100 IPR002126 Cadherin [Domain]
length(87), motif(45:131) 87 IPR002126 Cadherin [Domain]
length(20), motif(73:92) 20 IPR002126 Cadherin [Domain]
length(59), motif(75:133) 59 IPR002126 Cadherin [Domain]
length(11), motif(121:131) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(109), motif(126:234) 109 IPR015919 Cadherin-like [Domain]
length(110), motif(130:239) 110 IPR002126 Cadherin [Domain]
length(109), motif(134:242) 109 IPR002126 Cadherin [Domain]
length(94), motif(140:233) 94 IPR002126 Cadherin [Domain]
length(86), motif(155:240) 86 IPR002126 Cadherin [Domain]
length(11), motif(230:240) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(235:339) 105 IPR015919 Cadherin-like [Domain]
length(104), motif(240:343) 104 IPR002126 Cadherin [Domain]
length(30), motif(242:271) 30 IPR002126 Cadherin [Domain]
length(105), motif(243:347) 105 IPR002126 Cadherin [Domain]
length(91), motif(247:337) 91 IPR002126 Cadherin [Domain]
length(82), motif(264:345) 82 IPR002126 Cadherin [Domain]
length(13), motif(314:326) 13 IPR002126 Cadherin [Domain]
length(20), motif(326:345) 20 IPR002126 Cadherin [Domain]
length(11), motif(335:345) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(340:444) 105 IPR015919 Cadherin-like [Domain]
length(105), motif(344:448) 105 IPR002126 Cadherin [Domain]
length(105), motif(348:452) 105 IPR002126 Cadherin [Domain]
length(88), motif(355:442) 88 IPR002126 Cadherin [Domain]
length(82), motif(369:450) 82 IPR002126 Cadherin [Domain]
length(11), motif(440:450) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(110), motif(445:554) 110 IPR015919 Cadherin-like [Domain]
length(114), motif(449:562) 114 IPR002126 Cadherin [Domain]
length(14), motif(450:463) 14 IPR002126 Cadherin [Domain]
length(110), motif(453:562) 110 IPR002126 Cadherin [Domain]
length(96), motif(457:552) 96 IPR002126 Cadherin [Domain]
length(87), motif(474:560) 87 IPR002126 Cadherin [Domain]
length(27), motif(510:536) 27 IPR002126 Cadherin [Domain]
length(18), motif(544:561) 18 IPR002126 Cadherin [Domain]
length(11), motif(550:560) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(112), motif(555:666) 112 IPR015919 Cadherin-like [Domain]
length(89), motif(579:667) 89 IPR002126 Cadherin [Domain]
length(105), motif(579:683) 105 IPR002126 Cadherin [Domain]
length(83), motif(582:664) 83 IPR002126 Cadherin [Domain]
length(79), motif(591:669) 79 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000252990
H-Inv cluster ID Locus viewHIX0005252
Accession number AY358946.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-A12 isoform 2 precursor.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_115265)  [Identity/coverage = 100.0%/100.0%] 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 PCDHGA12
HGNC aliases "cadherin 21"
HGNC name protocadherin gamma subfamily A, 12
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 HIP000064974
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:26025; 
KEGG GENES KEGG GENES(26025); 
GeneCard GeneCardPCDHGA12;  *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 plasma membrane;  endoplasmic;  peroxisome; 
Target P signal peptide
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
34 96 1f5aA1 5e-14 15.8 57/118 d.58.16.1
73 178 1fx3A 2e-09 10.3 96/143 d.33.1.1
198 524 2nlzA1 5e-64 10.8 305/533 d.153.1.6
504 666 1o75A3 2e-14 7.5 152/191 b.120.1.1
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 AGhsA220313; 
Affymetrix
GeneChip		 HG-Focus 211875_x_at; 
HG-U133 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at; 
HG-U133A 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at; 
HG-U133A_2 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at; 
HG-U133B NA
HG-U133_Plus_2 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at; 
HG-U95 1691_at; 
HG-U95A 1691_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832657;  2832680;  2832681;  2832682;  2832683;  2832684;  2878651; 
HuGeneFL AB000897_at; 
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_24_P34944; 
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:(26025)
Disease Entrez Gene ID:(26025)
Substance Entrez Gene ID:(26025)
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
290 .. 290 T/C rs11575965 + 5'UTR
651 .. 651 A/G rs79193223 + CDS Nonsynonymous[Glu94Gly]
817 .. 817 G/A rs17097300 + CDS Synonymous[Glu149Glu]
932 .. 932 G/T rs112186927 + CDS Nonsynonymous[Gly188Cys]
1223 .. 1223 G/T rs79883194 + CDS Nonsynonymous[Asp285Tyr]
1379 .. 1379 G/A rs112978142 + CDS Nonsynonymous[Val337Ile]
1782 .. 1782 T/C rs114326665 + CDS Nonsynonymous[Leu471Pro]
2046 .. 2046 C/A rs78612001 + CDS Nonsynonymous[Ala559Glu]
2332 .. 2332 C/T rs13360857 + CDS Synonymous[Leu654Leu]
2455 .. 2455 A/G rs113107293 + CDS Synonymous[Val695Val]
2483 .. 2483 C/A rs73280906 + CDS Nonsynonymous[Leu705Met]
2641 .. 2641 T/C rs116611363 + CDS Synonymous[Val757Val]
2644 .. 2644 C/T rs115990854 + CDS Synonymous[Ser758Ser]
2927 .. 2927 C/T rs76825883 + CDS Nonsynonymous[Arg853Trp]
2939 ^ 2940 -/G rs34260612 + CDS
2973 ^ 2974 -/CTAT rs72463976 + CDS
2999 .. 3002 ATCT/- rs71692039 + CDS
3009 .. 3016 CTATCTAT/- rs71668367 + CDS
3013 ^ 3014 -/CTAT rs72479403 + CDS
3020 ^ 3021 -/CTAT rs3074541 + CDS
3021 .. 3021 T/C rs79220404 + CDS Nonsynonymous[Leu884Ser]
3022 .. 3022 A/T rs78298614 + CDS Nonsynonymous[Leu884Phe]
3312 .. 3312 C/A rs79404417 + 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
Location Variation Strand
2969..3020 (ctat)13 +
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
Type Start End Strand
FRAM 2811 2958 -
AluSp 3044 3313 +
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD); 
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer;