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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000071762 Accession number: AF152336 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Protocadherin gamma-B7; PCDH-gamma-B7; Precursor;
 
 

Transcript original information
Accession number AF152336.1
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 (PCDHGC5) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGC5);
Sequence data provider NA
Annotation project NA
Length of cDNA 4596[bp] (No. of exon:4)[A:1053 T:1008 G:1216 C:1319]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type brain
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) 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 140797427- 140892546
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 1..2790;  929[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.748
Database links RefSeq NP_061750
UniProt Q9Y5F8
CCDS CCDS47293

Motif information
ORF

length(929),orf(1:2790)
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(94), motif(355:448) 94 IPR002126 Cadherin [Domain]
length(88), motif(355:442) 88 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 HIT000071762
H-Inv cluster ID Locus viewHIX0005252
Accession number AF152336.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
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 PCDH-gamma-B7
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;  2832627;  2832628;  2832629;  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
151 .. 151 G/T rs185303697 + CDS Nonsynonymous[Ala51Ser]
193 .. 193 G/A rs202112422 + CDS Nonsynonymous[Glu65Lys]
197 .. 197 T/G rs199996434 + CDS Nonsynonymous[Leu66Arg]
204 .. 204 G/T rs2015825 + CDS Synonymous[Val68Val]
222 .. 222 C/T rs190197904 + CDS Synonymous[His74His]
262 .. 262 G/A rs201244691 + CDS Nonsynonymous[Asp88Asn]
284 .. 284 T/C rs200512171 + CDS Nonsynonymous[Ile95Thr]
343 ^ 344 -/C rs11386689 + CDS
387 .. 387 C/T rs200526306 + CDS Synonymous[His129His]
401 .. 401 G/A rs144490159 + CDS Nonsynonymous[Arg134Gln]
504 .. 504 C/T rs147423305 + CDS Synonymous[Ser168Ser]
537 .. 537 A/G rs139206858 + CDS Synonymous[Ser179Ser]
612 .. 612 G/T rs199547102 + CDS Synonymous[Thr204Thr]
639 .. 639 C/T rs181453589 + CDS Synonymous[Thr213Thr]
730 .. 730 C/G rs184213052 + CDS Nonsynonymous[Gln244Glu]
784 .. 784 C/A rs188546091 + CDS Nonsynonymous[Leu262Met]
938 .. 938 A/T rs201246978 + CDS Nonsynonymous[Glu313Val]
947 .. 947 C/T rs200530054 + CDS Nonsynonymous[Thr316Met]
951 .. 951 A/G rs149866479 + CDS Nonsynonymous[Ile317Met]
987 .. 987 A/G rs201160783 + CDS Synonymous[Thr329Thr]
1035 .. 1035 A/G rs200182481 + CDS Synonymous[Pro345Pro]
1046 .. 1046 T/C rs144920415 + CDS Nonsynonymous[Ile349Thr]
1063 .. 1063 C/G rs180948941 + CDS Nonsynonymous[Gln355Glu]
1205 .. 1205 A/G rs149057484 + CDS Nonsynonymous[Tyr402Cys]
1213 .. 1213 G/C rs17208397 + CDS Nonsynonymous[Val405Leu]
1243 .. 1243 A/G rs201327680 + CDS Nonsynonymous[Thr415Ala]
1316 .. 1316 C/A rs185228661 + CDS Nonsynonymous[Thr439Asn]
1344 .. 1344 C/T rs201698529 + CDS Synonymous[Asn448Asn]
1453 .. 1453 G/C rs35892780 + CDS Nonsynonymous[Gly485Arg]
1486 .. 1486 C/T rs111954647 + CDS Synonymous[Leu496Leu]
1491 .. 1491 G/T rs202038869 + CDS Nonsynonymous[Glu497Asp]
1566 .. 1566 C/T rs3749766 - CDS Synonymous[His522His]
1605 .. 1605 C/T rs199965876 + CDS Synonymous[Arg535Arg]
1621 .. 1621 G/T rs200408239 + CDS Nonsynonymous[Ala541Ser]
1646 .. 1646 G/A rs115850576 + CDS Nonsynonymous[Arg549His]
1697 .. 1697 C/A rs202164819 + CDS Nonsynonymous[Ala566Glu]
1779 .. 1779 C/T rs191182165 + CDS Synonymous[Ala593Ala]
1843 .. 1843 G/A rs116279995 + CDS Nonsynonymous[Gly615Arg]
1865 .. 1865 G/A rs200134846 + CDS Nonsynonymous[Arg622Gln]
1878 .. 1878 G/A rs201663350 + CDS Synonymous[Val626Val]
1880 .. 1880 G/A rs200899065 + CDS Nonsynonymous[Arg627His]
1892 .. 1892 C/T rs140649685 + CDS Nonsynonymous[Ala631Val]
2023 .. 2023 T/A rs145814583 + CDS Nonsynonymous[Phe675Ile]
2028 .. 2028 C/T rs200254467 + CDS Synonymous[Ser676Ser]
2105 .. 2105 T/C rs151105903 + CDS Nonsynonymous[Leu702Pro]
2121 .. 2121 G/T rs182372807 + CDS Synonymous[Val707Val]
2386 .. 2386 G/A rs72790042 + CDS Nonsynonymous[Val796Ile]
2395 .. 2395 G/C rs186977117 + CDS Nonsynonymous[Asp799His]
2452 .. 2452 G/A rs201391904 + CDS Nonsynonymous[Ala818Thr]
2464 .. 2464 G/A rs200418116 + CDS Nonsynonymous[Gly822Ser]
2520 .. 2520 T/C rs149352680 + CDS Synonymous[Phe840Phe]
2619 .. 2619 C/T rs143630962 + CDS Synonymous[Ser873Ser]
2620 .. 2620 G/A rs114669158 + CDS Nonsynonymous[Ala874Thr]
2623 .. 2623 C/T rs148119281 + CDS Nonsynonymous[Arg875Cys]
2628 .. 2628 C/T rs141873183 + CDS Synonymous[Tyr876Tyr]
2631 .. 2631 A/G rs2233612 + CDS Synonymous[Gly877Gly]
2653 .. 2653 G/A rs116366286 + CDS Nonsynonymous[Val885Met]
2666 .. 2666 G/A rs61749029 + CDS Nonsynonymous[Arg889His]
2693 .. 2693 A/G rs201009079 + CDS Nonsynonymous[Asn898Ser]
2709 .. 2709 C/T rs143362044 + CDS Synonymous[Asn903Asn]
2752 .. 2752 G/A rs200541479 + CDS Nonsynonymous[Gly918Ser]
2768 .. 2768 C/T rs202071188 + CDS Nonsynonymous[Ser923Leu]
2787 .. 2787 G/A rs147534370 + CDS Synonymous[Lys929Lys]
2819 .. 2819 C/T rs201024828 + 3'UTR
2820 .. 2820 G/A rs2233613 + 3'UTR
2925 .. 2925 G/A rs76613492 + 3'UTR
2981 .. 2981 T/C rs115159796 + 3'UTR
2991 .. 2991 C/A rs191106767 + 3'UTR
3227 .. 3227 C/A rs146235929 + 3'UTR
3245 .. 3245 G/C rs4912608 + 3'UTR
3320 .. 3320 T/G rs148447880 + 3'UTR
3482 .. 3482 G/A rs142624814 + 3'UTR
3503 .. 3503 T/C rs113814137 + 3'UTR
3509 .. 3509 C/T rs150999050 + 3'UTR
3516 .. 3516 T/G rs187622252 + 3'UTR
3705 .. 3705 A/G rs192947391 + 3'UTR
3788 .. 3788 T/C rs140884268 + 3'UTR
3811 .. 3811 G/A rs111365449 + 3'UTR
4002 .. 4002 A/G rs78180647 + 3'UTR
4070 .. 4070 G/A rs185198109 + 3'UTR
4163 .. 4163 C/T rs147780926 + 3'UTR
4456 .. 4456 C/T rs141207714 + 3'UTR
4475 .. 4475 G/T rs189734474 + 3'UTR
4531 .. 4531 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