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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000252990 Accession number: AY358946 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Protocadherin gamma-A12; PCDH-gamma-A12; Cadherin-21; Fibroblast cadherin-3; 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 ;
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 HIX0216314
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 NA
Ensembl NA
Entrez Gene Entrez Gene ID:26025
KEGG GENES KEGG GENES(26025)
GeneCard NA *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(70), motif(29:98) 70 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(108), motif(127:234) 108 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(119), motif(230:348) 119 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(125), motif(441:565) 125 IPR015919 Cadherin-like [Domain]
length(115), motif(449:563) 115 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(111), motif(556:666) 111 IPR015919 Cadherin-like [Domain]
length(88), motif(579:666) 88 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 viewHIX0216314
Accession number AY358946.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript; 
Coding potential  Help Protein coding; 
Definition Similar to Protocadherin gamma-A12; PCDH-gamma-A12; Cadherin-21; Fibroblast cadherin-3; Precursor;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (O60330)  [Identity/coverage = 100.0%/86.7%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 919919696285811038092912975309ALL
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol NA
HGNC aliases NA
HGNC name NA
DDBJ NA
UniProt PCDHGA12
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 NA
Ensembl NA
Entrez Gene Entrez Gene ID:26025
KEGG GENES KEGG GENES(26025)
GeneCard NA *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 Gene familyGene family;  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 cell adhesion (GO:0007155);  homophilic cell adhesion (GO:0007156); 
Cellular component membrane (GO:0016020);  plasma membrane (GO:0005886); 

Subcellular localization information  Last modified:27-May-2015
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:27-May-2015
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:27-May-2015
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

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
230 .. 230 A/G rs192473783 + 5'UTR
284 .. 284 C/T rs183365013 + 5'UTR
290 .. 290 T/C rs11575965 + 5'UTR
355 .. 355 C/G rs187713374 + 5'UTR
425 .. 425 C/T rs138641753 + CDS Nonsynonymous[Leu19Phe]
428 .. 428 C/T rs200369093 + CDS Synonymous[Leu20Leu]
465 .. 465 G/A rs140440273 + CDS Nonsynonymous[Arg32His]
537 .. 537 C/A rs145535410 + CDS Nonsynonymous[Pro56His]
562 .. 562 C/T rs200771871 + CDS Synonymous[Val64Val]
585 .. 585 C/T rs141488923 + CDS Nonsynonymous[Thr72Met]
618 .. 618 G/C rs149559471 + CDS Nonsynonymous[Ser83Thr]
622 .. 622 G/C rs144203659 + CDS Nonsynonymous[Leu84Phe]
651 .. 651 A/G rs79193223 + CDS Nonsynonymous[Glu94Gly]
663 .. 663 G/T rs148326556 + CDS Nonsynonymous[Gly98Val]
691 .. 691 C/T rs200757040 + CDS Synonymous[Asp107Asp]
699 .. 699 T/C rs143083513 + CDS Nonsynonymous[Met110Thr]
730 .. 730 A/C rs147514897 + CDS Nonsynonymous[Glu120Asp]
746 .. 746 A/G rs140069213 + CDS Nonsynonymous[Ile126Val]
751 .. 751 C/T rs145692116 + CDS Synonymous[Asn127Asn]
760 .. 760 G/A rs150692324 + CDS Synonymous[Ala130Ala]
814 .. 814 T/C rs139061906 + CDS Synonymous[Thr148Thr]
817 .. 817 G/A rs17097300 + CDS Synonymous[Glu149Glu]
911 .. 911 A/G rs200375087 + CDS Nonsynonymous[Ile181Val]
932 .. 932 G/T rs112186927 + CDS Nonsynonymous[Gly188Cys]
986 .. 986 G/T rs139873616 + CDS Nonsynonymous[Ala206Ser]
1006 .. 1006 T/A rs143252334 + CDS Synonymous[Leu212Leu]
1020 .. 1020 G/T rs146734417 + CDS Nonsynonymous[Gly217Val]
1064 .. 1064 G/A rs201704748 + CDS Nonsynonymous[Val232Ile]
1074 .. 1074 C/T rs139195027 + CDS Nonsynonymous[Ala235Val]
1140 .. 1140 T/C rs145601545 + CDS Nonsynonymous[Leu257Ser]
1195 .. 1195 G/C rs201462681 + CDS Synonymous[Ala275Ala]
1223 .. 1223 G/T rs79883194 + CDS Nonsynonymous[Asp285Tyr]
1266 .. 1266 G/A rs199998405 + CDS Nonsynonymous[Gly299Glu]
1379 .. 1379 G/A rs112978142 + CDS Nonsynonymous[Val337Ile]
1388 .. 1388 G/T rs151011884 + CDS Nonsynonymous[Val340Leu]
1429 .. 1429 C/T rs201311339 + CDS Synonymous[Ala353Ala]
1480 .. 1480 T/C rs140856757 + CDS Synonymous[Asn370Asn]
1549 .. 1549 A/G rs150199588 + CDS Synonymous[Lys393Lys]
1564 .. 1564 C/T rs188338684 + CDS Synonymous[Tyr398Tyr]
1609 .. 1609 A/G rs201105272 + CDS Synonymous[Glu413Glu]
1617 .. 1617 C/T rs138689793 + CDS Nonsynonymous[Pro416Leu]
1649 .. 1649 C/T rs202246871 + CDS Nonsynonymous[Arg427Trp]
1653 .. 1653 G/A rs143148175 + CDS Nonsynonymous[Gly428Glu]
1663 .. 1663 C/G rs192631651 + CDS Synonymous[Pro431Pro]
1676 .. 1676 A/C rs147057088 + CDS Nonsynonymous[Thr436Pro]
1690 .. 1690 G/A rs138510025 + CDS Synonymous[Leu440Leu]
1696 .. 1696 G/A rs144065251 + CDS Synonymous[Val442Val]
1699 .. 1699 A/T rs144317211 + CDS Synonymous[Ala443Ala]
1715 .. 1715 C/G rs199724525 + CDS Nonsynonymous[Pro449Ala]
1717 .. 1717 G/A rs148798222 + CDS Synonymous[Pro449Pro]
1782 .. 1782 T/C rs114326665 + CDS Nonsynonymous[Leu471Pro]
1807 .. 1807 C/G rs200790843 + CDS Synonymous[Pro479Pro]
1819 .. 1819 G/A rs150518735 + CDS Synonymous[Glu483Glu]
1858 .. 1858 C/G rs139910620 + CDS Nonsynonymous[Ile496Met]
1884 .. 1884 T/G rs199937628 + CDS Nonsynonymous[Val505Gly]
1893 .. 1893 A/G rs143317584 + CDS Nonsynonymous[Asn508Ser]
1898 .. 1898 G/A rs189131107 + CDS Nonsynonymous[Asp510Asn]
1946 .. 1946 C/T rs146691720 + CDS AA-STOP[Arg526*]
1989 .. 1989 C/T rs147564249 + CDS Nonsynonymous[Pro540Leu]
2005 .. 2005 C/T rs149830124 + CDS Synonymous[Asn545Asn]
2011 .. 2011 G/T rs139153105 + CDS Synonymous[Ser547Ser]
2046 .. 2046 C/A rs78612001 + CDS Nonsynonymous[Ala559Glu]
2065 .. 2065 C/T rs144987321 + CDS Synonymous[Pro565Pro]
2077 .. 2077 G/A rs149116648 + CDS Synonymous[Thr569Thr]
2104 .. 2104 T/G rs143178757 + CDS Synonymous[Ala578Ala]
2108 .. 2108 C/G rs201006002 + CDS Nonsynonymous[Arg580Gly]
2149 .. 2149 G/C rs200601557 + CDS Synonymous[Ala593Ala]
2151 .. 2151 T/A rs147884705 + CDS Nonsynonymous[Val594Glu]
2222 .. 2222 T/G rs141541670 + CDS Nonsynonymous[Ser618Ala]
2239 .. 2239 G/A rs200715621 + CDS Synonymous[Thr623Thr]
2292 .. 2292 G/A rs147073234 + CDS Nonsynonymous[Ser641Asn]
2294 .. 2294 C/T rs138402830 + CDS Nonsynonymous[Leu642Phe]
2299 .. 2299 A/G rs143889434 + CDS Synonymous[Val643Val]
2312 .. 2312 G/A rs200101512 + CDS Nonsynonymous[Asp648Asn]
2332 .. 2332 C/T rs13360857 + CDS Synonymous[Leu654Leu]
2353 .. 2353 C/A rs150249178 + CDS Synonymous[Thr661Thr]
2356 .. 2356 G/A rs138883931 + CDS Synonymous[Val662Val]
2427 .. 2427 C/A rs149438101 + CDS Nonsynonymous[Thr686Asn]
2455 .. 2455 A/G rs113107293 + CDS Synonymous[Val695Val]
2477 .. 2477 G/T rs139832920 + CDS Nonsynonymous[Val703Phe]
2483 .. 2483 C/A rs73280906 + CDS Nonsynonymous[Leu705Met]
2498 .. 2498 T/G rs146168033 + CDS Nonsynonymous[Leu710Val]
2511 .. 2511 T/A rs139221180 + CDS Nonsynonymous[Leu714His]
2551 .. 2551 T/C rs142546730 + CDS Synonymous[Ala727Ala]
2584 .. 2584 G/T rs150572360 + CDS Synonymous[Ser738Ser]
2641 .. 2641 T/C rs116611363 + CDS Synonymous[Val757Val]
2644 .. 2644 C/T rs115990854 + CDS Synonymous[Ser758Ser]
2783 .. 2783 G/C rs147848043 + CDS Nonsynonymous[Gly805Arg]
2792 .. 2792 G/T rs199507607 + CDS AA-STOP[Glu808*]
2900 .. 2900 C/T rs186668064 + CDS Nonsynonymous[Leu844Phe]
2927 .. 2927 C/T rs76825883 + CDS Nonsynonymous[Arg853Trp]
2937 ^ 2938 -/G rs34260612 + CDS
2973 ^ 2974 -/CTAT rs72463976 + CDS
3011 .. 3011 A/G rs189987785 + CDS Nonsynonymous[Ile881Val]
3015 .. 3015 A/C rs181247960 + CDS Nonsynonymous[Tyr882Ser]
3020 ^ 3021 -/CTAT rs3074541 + CDS
3127 .. 3127 A/G rs186288044 + 3'UTR
3312 .. 3312 C/A rs79404417 + 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
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