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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000053681 Accession number: BC051788 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Protocadherin gamma-B7; PCDH-gamma-B7; Precursor;
 
 

Transcript original information
Accession number BC051788.2
CAGE tag ID NA
EST ID NA
Clone Number MGC:57549 IMAGE:4941167
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 Provider:MGC/NCI
Annotation project H-Invitational FLcDNA
Length of cDNA 4771[bp] (No. of exon:4)[A:1092 T:1028 G:1263 C:1388]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Brain, anaplastic oligodendroglioma with 1p/19q loss
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 4757(+)
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 140797260- 140892513
Strand +
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56099
KEGG GENES KEGG GENES(56099)
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 HIP000056703
Predicted CDS 195..2984;  929[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.747
Database links RefSeq NP_061750
UniProt Q9Y5F8
CCDS CCDS47293

Motif information
ORF

length(929),orf(195:2984)
MGGSCAQRRRAGPRQVLFPLLLPLFYPTLCEPIRYSIPEELAKGSVVGNL
AKDLGLSVLDVSARELRVSAEKLHFSVDAQSGDLLVKDRIDREQICKERR
RCELQLEAVVENPLNIFHVIVVIEDVNDHAPQFRKDEINLEISESVSLGM
GTILESAEDPDISMNSLSKYQLSPNEYFSLVEKDNPDGGKYPELVLQKTL
DRETQSAHHLVLTALDGGDPPRSGTAQIRILVIDANDNPPVFSQDVYRVS
LREDVPPGTSILRVKATDQDEGINSEITYSFFGVADKAQHVFSLDYTTGN
ILTQQPLDFEEVERYTINIEAKDRGSLSTRCKVIVEVVDENDNSPEIIIT
SLSDQIMEDSPPGVVVALFKTRDQDSGENGEVRCSLSRGVPFKIHSSSNN
YYKLVTDEALDREQTPEYNVTIAATDRGKPPLSSSKTITLHITDVNDNAP
VFGQSAYLVHVPENNQPGASIAQVSASDPDFGLNGRVSYSLIASDLESRT
LSSYVSVSAQSGVVFAQRAFDHEQLRTFELTLQARDQGSPALSANVSLRV
LVGDRNDNAPRVLYPALGPDGSALFDTVPRAAQPGYLVTKVVAVDADSGH
NAWLSYHVVQASEPGLFSLGLRTGEVRMVRALGDKDSVRQRLLVAVRDGG
QPPLSATATLHLVFADSLQEVLPDFSDHPTPSDSQAEMQFYLVVALALIS
VLFLLAVILAIALRLRQSFSPTAGDCFESVLCSKSGPVGPPNYSEGTLPY
AYNFCVPGDQMNPEFNFFTSVDHCPATQDNLNKDSMLLASILTPSVEADK
KILKQQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMIL
ASASEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNAT
LTNAAGKRDGKAPAGGNGNKKKSGKKEKK*
a.a.
length
InterPro Name
length(101), motif(25:125) 101 IPR015919 Cadherin-like [Domain]
length(81), motif(32:112) 81 IPR013164 Cadherin, N-terminal [Domain]
length(93), motif(32:124) 93 IPR002126 Cadherin [Domain]
length(76), motif(56:131) 76 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(114), motif(125:238) 114 IPR002126 Cadherin [Domain]
length(108), motif(127:234) 108 IPR015919 Cadherin-like [Domain]
length(109), motif(134:242) 109 IPR002126 Cadherin [Domain]
length(92), motif(141:232) 92 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(109), motif(239:347) 109 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(11), motif(335:345) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(104), motif(341:444) 104 IPR015919 Cadherin-like [Domain]
length(105), motif(348:452) 105 IPR002126 Cadherin [Domain]
length(88), motif(355:442) 88 IPR002126 Cadherin [Domain]
length(94), motif(355:448) 94 IPR002126 Cadherin [Domain]
length(82), motif(369:450) 82 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(123), motif(441:563) 123 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(109), motif(556:664) 109 IPR015919 Cadherin-like [Domain]
length(90), motif(577:666) 90 IPR002126 Cadherin [Domain]
length(99), motif(577:675) 99 IPR002126 Cadherin [Domain]
length(82), motif(580:661) 82 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 HIT000053681
H-Inv cluster ID Locus viewHIX0005252
Accession number BC051788.2
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-B7; PCDH-gamma-B7; Precursor;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q9Y5F8)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 1038092915489334ALL
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 PCDHGB7
UniProt PCDHGB7
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 HIP000056703
No. of interaction 2
Interaction partner(s) HIP000042582HIP000042582
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56099
KEGG GENES KEGG GENES(56099)
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
34 97 1f5aA1 6e-14 21.7 60/118 d.58.16.1
75 166 2fwuA1 5e-09 19.6 88/157 b.1.27.1
198 602 1dnvA 3e-71 9.7 372/415 b.121.5.3
584 661 1edhA1 2e-12 9.8 78/99 b.1.6.1
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 AGhsA110116;  AGhsB190717; 
Affymetrix
GeneChip
HG-Focus 215836_s_at; 
HG-U133 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133A 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133A_2 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133B NA
HG-U133_Plus_2 1552662_a_at;  205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U95 1169_at;  657_at; 
HG-U95A 1169_at;  657_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832573;  2832626;  2832627;  2832628;  2832629;  2832646;  2832647;  2832648;  2832649;  2832650;  2832651;  2832751;  2832754;  2832758;  2832759;  2832760;  2832761;  2832762;  2832763;  2832764;  2832765;  2832766;  2832767;  2832768;  2832769;  2878647;  2878649;  2878661; 
HuGeneFL D88799_at;  L11373_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P354734; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P354734; 
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
107 .. 107 A/C rs2240701 + 5'UTR
153 .. 153 C/T rs59981184 + 5'UTR
345 .. 345 G/T rs185303697 + CDS Nonsynonymous[Ala51Ser]
387 .. 387 G/A rs202112422 + CDS Nonsynonymous[Glu65Lys]
391 .. 391 T/G rs199996434 + CDS Nonsynonymous[Leu66Arg]
398 .. 398 T/G rs2015825 + CDS Synonymous[Val68Val]
416 .. 416 C/T rs190197904 + CDS Synonymous[His74His]
456 .. 456 G/A rs201244691 + CDS Nonsynonymous[Asp88Asn]
478 .. 478 T/C rs200512171 + CDS Nonsynonymous[Ile95Thr]
537 ^ 538 -/C rs11386689 + CDS
581 .. 581 C/T rs200526306 + CDS Synonymous[His129His]
595 .. 595 G/A rs144490159 + CDS Nonsynonymous[Arg134Gln]
698 .. 698 C/T rs147423305 + CDS Synonymous[Ser168Ser]
731 .. 731 A/G rs139206858 + CDS Synonymous[Ser179Ser]
806 .. 806 G/T rs199547102 + CDS Synonymous[Thr204Thr]
833 .. 833 C/T rs181453589 + CDS Synonymous[Thr213Thr]
924 .. 924 C/G rs184213052 + CDS Nonsynonymous[Gln244Glu]
978 .. 978 C/A rs188546091 + CDS Nonsynonymous[Leu262Met]
1132 .. 1132 A/T rs201246978 + CDS Nonsynonymous[Glu313Val]
1141 .. 1141 C/T rs200530054 + CDS Nonsynonymous[Thr316Met]
1145 .. 1145 A/G rs149866479 + CDS Nonsynonymous[Ile317Met]
1181 .. 1181 A/G rs201160783 + CDS Synonymous[Thr329Thr]
1229 .. 1229 A/G rs200182481 + CDS Synonymous[Pro345Pro]
1240 .. 1240 T/C rs144920415 + CDS Nonsynonymous[Ile349Thr]
1257 .. 1257 C/G rs180948941 + CDS Nonsynonymous[Gln355Glu]
1399 .. 1399 A/G rs149057484 + CDS Nonsynonymous[Tyr402Cys]
1407 .. 1407 G/C rs17208397 + CDS Nonsynonymous[Val405Leu]
1437 .. 1437 A/G rs201327680 + CDS Nonsynonymous[Thr415Ala]
1510 .. 1510 C/A rs185228661 + CDS Nonsynonymous[Thr439Asn]
1538 .. 1538 C/T rs201698529 + CDS Synonymous[Asn448Asn]
1647 .. 1647 G/C rs35892780 + CDS Nonsynonymous[Gly485Arg]
1680 .. 1680 C/T rs111954647 + CDS Synonymous[Leu496Leu]
1685 .. 1685 G/T rs202038869 + CDS Nonsynonymous[Glu497Asp]
1760 .. 1760 C/T rs3749766 - CDS Synonymous[His522His]
1799 .. 1799 C/T rs199965876 + CDS Synonymous[Arg535Arg]
1815 .. 1815 G/T rs200408239 + CDS Nonsynonymous[Ala541Ser]
1840 .. 1840 G/A rs115850576 + CDS Nonsynonymous[Arg549His]
1891 .. 1891 C/A rs202164819 + CDS Nonsynonymous[Ala566Glu]
1973 .. 1973 C/T rs191182165 + CDS Synonymous[Ala593Ala]
2037 .. 2037 G/A rs116279995 + CDS Nonsynonymous[Gly615Arg]
2059 .. 2059 G/A rs200134846 + CDS Nonsynonymous[Arg622Gln]
2072 .. 2072 G/A rs201663350 + CDS Synonymous[Val626Val]
2074 .. 2074 G/A rs200899065 + CDS Nonsynonymous[Arg627His]
2086 .. 2086 C/T rs140649685 + CDS Nonsynonymous[Ala631Val]
2217 .. 2217 T/A rs145814583 + CDS Nonsynonymous[Phe675Ile]
2222 .. 2222 C/T rs200254467 + CDS Synonymous[Ser676Ser]
2299 .. 2299 T/C rs151105903 + CDS Nonsynonymous[Leu702Pro]
2315 .. 2315 G/T rs182372807 + CDS Synonymous[Val707Val]
2580 .. 2580 G/A rs72790042 + CDS Nonsynonymous[Val796Ile]
2589 .. 2589 G/C rs186977117 + CDS Nonsynonymous[Asp799His]
2646 .. 2646 G/A rs201391904 + CDS Nonsynonymous[Ala818Thr]
2658 .. 2658 G/A rs200418116 + CDS Nonsynonymous[Gly822Ser]
2714 .. 2714 T/C rs149352680 + CDS Synonymous[Phe840Phe]
2813 .. 2813 C/T rs143630962 + CDS Synonymous[Ser873Ser]
2814 .. 2814 G/A rs114669158 + CDS Nonsynonymous[Ala874Thr]
2817 .. 2817 C/T rs148119281 + CDS Nonsynonymous[Arg875Cys]
2822 .. 2822 C/T rs141873183 + CDS Synonymous[Tyr876Tyr]
2825 .. 2825 A/G rs2233612 + CDS Synonymous[Gly877Gly]
2847 .. 2847 G/A rs116366286 + CDS Nonsynonymous[Val885Met]
2860 .. 2860 G/A rs61749029 + CDS Nonsynonymous[Arg889His]
2887 .. 2887 A/G rs201009079 + CDS Nonsynonymous[Asn898Ser]
2903 .. 2903 C/T rs143362044 + CDS Synonymous[Asn903Asn]
2946 .. 2946 G/A rs200541479 + CDS Nonsynonymous[Gly918Ser]
2962 .. 2962 C/T rs202071188 + CDS Nonsynonymous[Ser923Leu]
2981 .. 2981 G/A rs147534370 + CDS Synonymous[Lys929Lys]
3013 .. 3013 C/T rs201024828 + 3'UTR
3014 .. 3014 A/G rs2233613 + 3'UTR
3119 .. 3119 G/A rs76613492 + 3'UTR
3175 .. 3175 T/C rs115159796 + 3'UTR
3185 .. 3185 C/A rs191106767 + 3'UTR
3421 .. 3421 C/A rs146235929 + 3'UTR
3439 .. 3439 G/C rs4912608 + 3'UTR
3514 .. 3514 T/G rs148447880 + 3'UTR
3676 .. 3676 G/A rs142624814 + 3'UTR
3697 .. 3697 T/C rs113814137 + 3'UTR
3703 .. 3703 C/T rs150999050 + 3'UTR
3710 .. 3710 T/G rs187622252 + 3'UTR
3899 .. 3899 A/G rs192947391 + 3'UTR
3982 .. 3982 T/C rs140884268 + 3'UTR
4005 .. 4005 G/A rs111365449 + 3'UTR
4196 .. 4196 A/G rs78180647 + 3'UTR
4264 .. 4264 G/A rs185198109 + 3'UTR
4357 .. 4357 C/T rs147780926 + 3'UTR
4650 .. 4650 C/T rs141207714 + 3'UTR
4669 .. 4669 G/T rs189734474 + 3'UTR
4725 .. 4725 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