H-InvDB x AHG DB
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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000435698 Accession number: BC150172 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Protocadherin gamma-B3; PCDH-gamma-B3; Precursor;
 
 

Transcript original information
Accession number BC150172.1
CAGE tag ID NA
EST ID NA
Clone Number MGC:164749 IMAGE:40147143
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PCDHGC5) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGC5);
Sequence data provider NA
Annotation project NA
Length of cDNA 4758[bp] (No. of exon:4)[A:1141 T:1029 G:1220 C:1368]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Donated clones,Novartis FGA collection
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 4720(+) Signal: 4702-4706(+)
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 140749831- 140892539
Strand +
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56102
KEGG GENES KEGG GENES(56102)
GeneCard GeneCardPCDHGC5*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 HIP000199767
Predicted CDS 132..2921;  929[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.764
Database links RefSeq NA
UniProt NA
CCDS CCDS58980

Motif information
ORF

length(929),orf(132:2921)
MGNSSGWRGPAGQRRMLFLFLLSLLDQALSEPIRYAIPEELDRGSLVGNL
AKDLGFGVGDLPTRNLRVIAEKKFFTVSPENGNLLVSDRIDREEICGKKS
TCVLEFEMVAEKPLNFFHVTVLIQDINDNPPTFSQNITELEISELALTGA
TFALESAQDPDVGVNSLQQYYLSPDPHFSLIQKENLDGSRYPELVLKAPL
DREEQPHHHLVLTAVDGGEPSRSCTTQIRVIVADANDNPPVFTQDMYRVN
VAENLPAGSSVLKVMAIDMDEGINAEIIYAFINIGKEVRQLFKLDSKTGE
LTTIGELDFEERDSYTIGVEAKDGGHHTAYCKVQIDISDENDNAPEITLA
SESQHIQEDAELGTAVALIKTHDLDSGFNGEILCQLKGNFPFKIVQDTKN
TYRLVTDGALDREQIPEYNVTITATDKGNPPLSSSKTITLHILDVNDNVP
VFHQASYTVHVAENNPPGASIAHVRASDPDLGPNGLVSYYIVASDLEPRE
LSSYVSVSARSGVVFAQRAFDHEQLRAFELTLQARDQGSPTLSANVSLRV
LVDDRNDNAPLVLYPALGPEGSALFDMVPRSAEPGYLVTKVVAVDADSGY
NAWLSYHIVQASEPGLFSLGLRTGEVRTARTLGDREAARQRLLVTVRDGG
QQPLSATVMLHLIFADSLQEIQPDLSDRPTPSDPQAELQFHLVVALALIS
VLFLLAVILAISLRLRCSSRPATEGYFQPGVCFKTVPGVLPTYSERTLPY
SYNPCAASHSSNTEFKFLNIKAENAAPQDLLCDEASWFESNDNPEMPSNS
GNLQKQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMIL
ASASEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNAT
LTNAAGKRDGKAPAGGNGNKKKSGKKEKK*
a.a.
length
InterPro Name
length(112), motif(20:131) 112 IPR002126 Cadherin [Domain]
length(108), motif(26:133) 108 IPR002126 Cadherin [Domain]
length(95), motif(31:125) 95 IPR015919 Cadherin-like [Domain]
length(81), motif(32:112) 81 IPR013164 Cadherin, N-terminal [Domain]
length(61), motif(69:129) 61 IPR002126 Cadherin [Domain]
length(20), motif(73:92) 20 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(93), motif(140:232) 93 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(11), motif(335:345) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(104), motif(341:444) 104 IPR015919 Cadherin-like [Domain]
length(105), motif(344:448) 105 IPR002126 Cadherin [Domain]
length(105), motif(348:452) 105 IPR002126 Cadherin [Domain]
length(89), motif(355:443) 89 IPR002126 Cadherin [Domain]
length(82), motif(369:450) 82 IPR002126 Cadherin [Domain]
length(13), motif(417:429) 13 IPR002126 Cadherin [Domain]
length(20), motif(431:450) 20 IPR002126 Cadherin [Domain]
length(11), motif(440:450) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(124), motif(441:564) 124 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(108), motif(556:663) 108 IPR015919 Cadherin-like [Domain]
length(98), motif(578:675) 98 IPR002126 Cadherin [Domain]
length(89), motif(578:666) 89 IPR002126 Cadherin [Domain]
length(81), motif(581:661) 81 IPR002126 Cadherin [Domain]
length(82), motif(591:672) 82 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000435698
H-Inv cluster ID Locus viewHIX0005252
Accession number BC150172.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-B3; PCDH-gamma-B3; Precursor;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q9Y5G1)  [Identity/coverage = 99.892%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 103809291537202215489334ALL
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 PCDHGC5
HGNC aliases NA
HGNC name protocadherin gamma subfamily C, 5
DDBJ PCDHGB3
UniProt PCDHGB3
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 HIP000199767
No. of interaction 11
Interaction partner(s) HIP000010782HIP000031442HIP000032747HIP000046840HIP000048574HIP000079553HIP000082159HIP000085884HIP000110009HIP000110470HIP000122282
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56102
KEGG GENES KEGG GENES(56102)
GeneCard GeneCardPCDHGC5*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 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 extracellular;  plasma membrane;  peroxisome;  Other; 
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
5 97 1f5aA1 9e-18 15.7 89/118 d.58.16.1
73 181 1nkgA2 9e-10 8.9 103/171 b.18.1.25
199 610 1dnvA 1e-66 8.7 379/415 b.121.5.3
581 661 1f15A 5e-11 8.5 75/157 b.121.4.5
Related H-InvDB links GTOP GTOP

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
18 .. 18 A/G rs184302654 + 5'UTR
125 .. 125 G/A rs10052885 + 5'UTR
135 .. 135 G/A rs189405542 + CDS Nonsynonymous[Gly2Arg]
154 .. 154 G/A rs74964649 + CDS Nonsynonymous[Arg8Lys]
155 .. 155 G/A rs145463208 + CDS Synonymous[Arg8Arg]
190 .. 190 T/A rs6860590 + CDS Nonsynonymous[Phe20Tyr]
214 .. 214 C/T rs6860609 + CDS Nonsynonymous[Ala28Val]
397 .. 397 G/T rs199537402 + CDS Nonsynonymous[Arg89Leu]
466 .. 466 A/T rs73265845 + CDS Nonsynonymous[Lys112Met]
557 .. 557 C/T rs140287572 + CDS Synonymous[Ile142Ile]
590 .. 590 C/T rs73265846 + CDS Synonymous[Ala153Ala]
609 .. 609 C/T rs201155008 + CDS Nonsynonymous[Pro160Ser]
630 .. 630 C/G rs116495533 + CDS Nonsynonymous[Leu167Val]
687 .. 687 C/T rs78666647 + CDS Synonymous[Leu186Leu]
720 .. 720 A/G rs200655179 + CDS Nonsynonymous[Lys197Glu]
767 .. 767 C/T rs62378420 + CDS Synonymous[Leu212Leu]
844 .. 844 A/G rs202073589 + CDS Nonsynonymous[Asn238Ser]
880 .. 880 A/G rs199674539 + CDS Nonsynonymous[Asn250Ser]
882 .. 882 G/A rs144065486 + CDS Nonsynonymous[Val251Ile]
900 .. 900 G/C rs79773129 + CDS Nonsynonymous[Ala257Pro]
941 .. 941 T/C rs141363854 + CDS Synonymous[Asp270Asp]
946 .. 946 G/A rs143352621 + CDS Nonsynonymous[Gly272Asp]
1019 .. 1019 T/G rs201701201 + CDS Nonsynonymous[Ser296Arg]
1038 .. 1038 A/G rs199851082 + CDS Nonsynonymous[Thr303Ala]
1070 .. 1070 T/G rs201139834 + CDS Nonsynonymous[Asp313Glu]
1109 .. 1109 T/A rs73265849 + CDS Nonsynonymous[His326Gln]
1137 .. 1137 G/C rs201084970 + CDS Nonsynonymous[Asp336His]
1199 .. 1199 A/G rs181808735 + CDS Nonsynonymous[Ile356Met]
1266 .. 1266 A/G rs200031435 + CDS Nonsynonymous[Asn379Asp]
1298 .. 1298 C/G rs2240697 + CDS Nonsynonymous[Asn389Lys]
1314 .. 1314 G/A rs202142331 + CDS Nonsynonymous[Val395Ile]
1415 .. 1415 C/G rs200964276 + CDS Synonymous[Gly428Gly]
1424 .. 1424 G/C rs201325462 + CDS Synonymous[Pro431Pro]
1432 .. 1432 C/T rs186000917 + CDS Nonsynonymous[Ser434Phe]
1458 .. 1458 C/T rs199558038 + CDS Nonsynonymous[Leu443Phe]
1510 .. 1510 A/C rs148367405 + CDS Nonsynonymous[His460Pro]
1529 .. 1529 G/T rs190449546 + CDS Synonymous[Pro466Pro]
1559 .. 1559 C/T rs3749776 - CDS Synonymous[Ala476Ala]
1583 .. 1583 T/A rs201850389 + CDS Nonsynonymous[Asn484Lys]
1617 .. 1617 C/G rs62378421 + CDS Nonsynonymous[Leu496Val]
1659 .. 1659 C/T rs200368368 + CDS Nonsynonymous[Arg510Trp]
1683 .. 1683 C/T rs200127619 + CDS AA-STOP[Arg518*]
1685 .. 1685 A/C rs200505160 + CDS Synonymous[Arg518Arg]
1839 .. 1839 G/A rs200898659 + CDS Nonsynonymous[Glu570Lys]
1866 .. 1866 C/A rs62620756 + CDS Nonsynonymous[Pro579Thr]
1868 .. 1868 G/A rs181587030 + CDS Synonymous[Pro579Pro]
1934 .. 1934 C/T rs57763341 + CDS Synonymous[Asn601Asn]
1970 .. 1970 G/A rs140609729 + CDS Synonymous[Glu613Glu]
2010 .. 2010 C/A rs201775561 + CDS Nonsynonymous[Arg627Ser]
2023 .. 2023 C/T rs62620706 + CDS Nonsynonymous[Thr631Ile]
2036 .. 2036 G/T rs35459734 + CDS Nonsynonymous[Arg635Ser]
2274 .. 2274 C/A rs138338803 + CDS Nonsynonymous[Leu715Met]
2421 .. 2421 G/A rs199934753 + CDS Nonsynonymous[Glu764Lys]
2491 .. 2491 G/A rs201408759 + CDS AA-STOP[Trp787*]
2583 .. 2583 G/A rs201391904 + CDS Nonsynonymous[Ala818Thr]
2595 .. 2595 G/A rs200418116 + CDS Nonsynonymous[Gly822Ser]
2651 .. 2651 T/C rs149352680 + CDS Synonymous[Phe840Phe]
2750 .. 2750 C/T rs143630962 + CDS Synonymous[Ser873Ser]
2751 .. 2751 G/A rs114669158 + CDS Nonsynonymous[Ala874Thr]
2754 .. 2754 C/T rs148119281 + CDS Nonsynonymous[Arg875Cys]
2759 .. 2759 C/T rs141873183 + CDS Synonymous[Tyr876Tyr]
2762 .. 2762 A/G rs2233612 + CDS Synonymous[Gly877Gly]
2784 .. 2784 G/A rs116366286 + CDS Nonsynonymous[Val885Met]
2797 .. 2797 G/A rs61749029 + CDS Nonsynonymous[Arg889His]
2824 .. 2824 A/G rs201009079 + CDS Nonsynonymous[Asn898Ser]
2840 .. 2840 C/T rs143362044 + CDS Synonymous[Asn903Asn]
2883 .. 2883 G/A rs200541479 + CDS Nonsynonymous[Gly918Ser]
2899 .. 2899 C/T rs202071188 + CDS Nonsynonymous[Ser923Leu]
2918 .. 2918 G/A rs147534370 + CDS Synonymous[Lys929Lys]
2950 .. 2950 C/T rs201024828 + 3'UTR
2951 .. 2951 G/A rs2233613 + 3'UTR
3056 .. 3056 G/A rs76613492 + 3'UTR
3112 .. 3112 T/C rs115159796 + 3'UTR
3122 .. 3122 C/A rs191106767 + 3'UTR
3358 .. 3358 C/A rs146235929 + 3'UTR
3376 .. 3376 G/C rs4912608 + 3'UTR
3451 .. 3451 T/G rs148447880 + 3'UTR
3613 .. 3613 G/A rs142624814 + 3'UTR
3634 .. 3634 T/C rs113814137 + 3'UTR
3640 .. 3640 C/T rs150999050 + 3'UTR
3647 .. 3647 T/G rs187622252 + 3'UTR
3836 .. 3836 A/G rs192947391 + 3'UTR
3919 .. 3919 T/C rs140884268 + 3'UTR
3942 .. 3942 G/A rs111365449 + 3'UTR
4133 .. 4133 A/G rs78180647 + 3'UTR
4201 .. 4201 G/A rs185198109 + 3'UTR
4294 .. 4294 C/T rs147780926 + 3'UTR
4587 .. 4587 C/T rs141207714 + 3'UTR
4606 .. 4606 G/T rs189734474 + 3'UTR
4662 .. 4662 C/T rs112402554 + 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