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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000071808 Accession number: AF152504 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Protocadherin gamma-A11; PCDH-gamma-A11; Precursor;
 
 

Transcript original information
Accession number AF152504.1
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 2262[bp] (No. of exon:4)[A:563 T:478 G:618 C:603]
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) 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 140800795- 140890747
Strand +
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56105
KEGG GENES KEGG GENES(56105)
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 HIP000030816
Predicted CDS 1..2253;  750[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.766
Database links RefSeq NP_114481
UniProt NA
CCDS CCDS54930

Motif information
ORF

length(750),orf(1:2253)
MANRLQRGDRSRLLLLLCIFLGTLRGFRARQIRYSVPEETEKGSFVGNIS
KDLGLEPRELAKRGVRIVSRGKTQLFAVNPRSGSLITAGRIDREELCETV
SSCFLNMELLVEDTLKIYGVEVEIIDINDNAPSFQEDEVEIKVSEHAIPG
ARFALPNARDPDVGVNSLQSYQLSPNNYFSLQLRGRTDGAKNPELVLEGS
LDREKEAAHLLLLTALDGGDPIRKGAVPIRVVVLDVNDHIPMFTQSVYRV
SVPENISSGTRVLMVNATDPDEGINGEVMYSFRNMESKASEIFQLDSQTG
EVQVRGSLDFEKYRFYEMEIQGQDGGGLFTTTTMLITVVDVNDNAPEITI
TSSINSILENSPPGTVIALLNVQDQDSGENGQVSCFIPNHLPFKLEKTYG
NYYKLITSRVLDRELVQSYNITLTATDQGSPPLSAETHVWLNVADDNDNP
PVFPHSSYSAYIPENNPRGASIFSVTALDPDSKQNALVTYSLTDDTVQGV
PLSSYVSINSNTGVLYALQSFDYEQFRDLELRVIARDSGDPPLSSNVSLS
LFVLDQNDNAPEILYPALPTDGSTGVELAPRSAEPGYLVTKVVAVDKDSG
QNAWLSYRLLKASEPGLFAVGEHTGEQAPPNTDWRFSQAQRPGTSGSQNG
DDTGTWPNNQFDTEMLQAMILASASEAADGSSTLGGGAGTMGLSARYGPQ
FTLQHVPDYRQNVYIPGSNATLTNAAGKRDGKAPAGGNGNKKKSGKKEKK
*
a.a.
length
InterPro Name
length(72), motif(27:98) 72 IPR015919 Cadherin-like [Domain]
length(81), motif(27:107) 81 IPR002126 Cadherin [Domain]
length(107), motif(28:134) 107 IPR002126 Cadherin [Domain]
length(83), motif(31:113) 83 IPR013164 Cadherin, N-terminal [Domain]
length(101), motif(32:132) 101 IPR002126 Cadherin [Domain]
length(20), motif(74:93) 20 IPR002126 Cadherin [Domain]
length(11), motif(122:132) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(116), motif(125:240) 116 IPR002126 Cadherin [Domain]
length(108), motif(128:235) 108 IPR015919 Cadherin-like [Domain]
length(109), motif(135:243) 109 IPR002126 Cadherin [Domain]
length(86), motif(156:241) 86 IPR002126 Cadherin [Domain]
length(11), motif(231:241) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(130), motif(231:360) 130 IPR015919 Cadherin-like [Domain]
length(104), motif(241:344) 104 IPR002126 Cadherin [Domain]
length(30), motif(243:272) 30 IPR002126 Cadherin [Domain]
length(105), motif(244:348) 105 IPR002126 Cadherin [Domain]
length(91), motif(248:338) 91 IPR002126 Cadherin [Domain]
length(82), motif(265:346) 82 IPR002126 Cadherin [Domain]
length(13), motif(315:327) 13 IPR002126 Cadherin [Domain]
length(20), motif(327:346) 20 IPR002126 Cadherin [Domain]
length(11), motif(336:346) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(341:445) 105 IPR015919 Cadherin-like [Domain]
length(105), motif(345:449) 105 IPR002126 Cadherin [Domain]
length(105), motif(349:453) 105 IPR002126 Cadherin [Domain]
length(88), motif(356:443) 88 IPR002126 Cadherin [Domain]
length(82), motif(370:451) 82 IPR002126 Cadherin [Domain]
length(11), motif(441:451) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(125), motif(442:566) 125 IPR015919 Cadherin-like [Domain]
length(115), motif(450:564) 115 IPR002126 Cadherin [Domain]
length(14), motif(451:464) 14 IPR002126 Cadherin [Domain]
length(110), motif(454:563) 110 IPR002126 Cadherin [Domain]
length(96), motif(458:553) 96 IPR002126 Cadherin [Domain]
length(87), motif(475:561) 87 IPR002126 Cadherin [Domain]
length(27), motif(511:537) 27 IPR002126 Cadherin [Domain]
length(18), motif(545:562) 18 IPR002126 Cadherin [Domain]
length(11), motif(551:561) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(71), motif(557:627) 71 IPR015919 Cadherin-like [Domain]
length(47), motif(580:626) 47 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000071808
H-Inv cluster ID Locus viewHIX0005252
Accession number AF152504.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-A11; PCDH-gamma-A11; Precursor;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q9Y5H2)  [Identity/coverage = 99.867%/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-A11
UniProt PCDHGA11
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 HIP000030816
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:56105
KEGG GENES KEGG GENES(56105)
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;  mitochondria;  lysosome;  Other; 
Target P mitochondria
SOSUI soluble protein
TMHMM membrane protein
PTS1 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
31 97 1f5aA1 2e-18 19.7 61/118 d.58.16.1
74 167 2fwuA1 4e-09 14.1 90/157 b.1.27.1
202 525 2nlzA1 6e-66 14.2 302/533 d.153.1.6
505 626 1o75A3 4e-11 7.5 115/191 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 NA
Affymetrix
GeneChip
HG-Focus NA
HG-U133 211876_x_at;  216352_x_at; 
HG-U133A 211876_x_at;  216352_x_at; 
HG-U133A_2 211876_x_at;  216352_x_at; 
HG-U133B NA
HG-U133_Plus_2 211876_x_at;  216352_x_at; 
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832655;  2832656;  2832751;  2832754;  2832758;  2832759;  2832760;  2832761;  2878647;  2878650; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 NA
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
6 .. 6 G/A rs201076931 + CDS Synonymous[Ala2Ala]
16 .. 16 C/A rs201273667 + CDS Nonsynonymous[Gln6Lys]
60 ^ 61 -/C rs35600583 + CDS
70 .. 70 C/T rs143092131 + CDS Synonymous[Leu24Leu]
84 .. 84 G/A rs199877605 + CDS Synonymous[Arg28Arg]
86 .. 86 C/T rs201429116 + CDS Nonsynonymous[Ala29Val]
115 .. 115 G/A rs199737254 + CDS Nonsynonymous[Glu39Lys]
120 .. 120 C/T rs147068995 + CDS Synonymous[Thr40Thr]
121 .. 121 G/C rs202220769 + CDS Nonsynonymous[Glu41Gln]
162 .. 162 G/A rs200646513 + CDS Synonymous[Gly54Gly]
289 .. 289 T/G rs199973694 + CDS Nonsynonymous[Cys97Gly]
306 .. 306 C/T rs80184002 + CDS Synonymous[Ser102Ser]
310 .. 310 T/C rs11167744 + CDS Nonsynonymous[Phe104Leu]
368 .. 368 A/G rs77665158 + CDS Nonsynonymous[Glu123Gly]
399 .. 399 C/G rs201673318 + CDS Nonsynonymous[Ser133Arg]
504 .. 504 C/A rs73792198 + CDS Synonymous[Leu168Leu]
604 .. 604 G/C rs201283981 + CDS Nonsynonymous[Asp202His]
632 .. 632 T/C rs138408376 + CDS Nonsynonymous[Leu211Pro]
642 .. 642 A/G rs200015978 + CDS Synonymous[Thr214Thr]
714 .. 714 T/C rs186605459 + CDS Synonymous[Asp238Asp]
726 .. 726 G/A rs193141134 + CDS Nonsynonymous[Met242Ile]
757 .. 757 C/G rs201871921 + CDS Nonsynonymous[Pro253Ala]
784 .. 784 G/T rs200879435 + CDS Nonsynonymous[Val262Leu]
799 .. 799 G/A rs118080774 + CDS Nonsynonymous[Ala267Thr]
977 .. 977 G/A rs185669562 + CDS Nonsynonymous[Gly326Glu]
1069 .. 1069 A/G rs200545713 + CDS Nonsynonymous[Ile357Val]
1082 .. 1082 C/T rs199660151 + CDS Nonsynonymous[Ser361Phe]
1103 .. 1103 C/T rs200342957 + CDS Nonsynonymous[Ala368Val]
1156 .. 1156 T/C rs201301291 + CDS Nonsynonymous[Phe386Leu]
1208 .. 1208 A/G rs199795822 + CDS Nonsynonymous[Tyr403Cys]
1209 .. 1209 C/T rs200737047 + CDS Synonymous[Tyr403Tyr]
1405 .. 1405 G/T rs199543811 + CDS Nonsynonymous[Gly469Cys]
1428 .. 1428 C/T rs188587553 + CDS Synonymous[Thr476Thr]
1522 .. 1522 A/G rs202046219 + CDS Nonsynonymous[Ile508Val]
1580 .. 1580 G/A rs199507728 + CDS Nonsynonymous[Arg527Gln]
1605 .. 1605 A/G rs12520854 + CDS Synonymous[Ala535Ala]
1611 .. 1611 C/T rs201218542 + CDS Synonymous[Asp537Asp]
1623 .. 1623 G/A rs184432819 + CDS Synonymous[Pro541Pro]
1640 .. 1640 T/C rs116031289 + CDS Nonsynonymous[Val547Ala]
1657 .. 1657 G/C rs202035589 + CDS Nonsynonymous[Val553Leu]
1662 .. 1662 G/A rs62378455 + CDS Synonymous[Leu554Leu]
1693 .. 1693 T/G rs13173779 + CDS Nonsynonymous[Tyr565Asp]
1696 .. 1696 C/T rs188787674 + CDS Nonsynonymous[Pro566Ser]
1704 .. 1704 C/T rs13188208 + CDS Synonymous[Leu568Leu]
1715 .. 1715 G/T rs199976232 + CDS Nonsynonymous[Gly572Val]
1716 .. 1716 C/G rs13188214 + CDS Synonymous[Gly572Gly]
1718 .. 1718 C/T rs13188215 + CDS Nonsynonymous[Ser573Phe]
1770 .. 1770 C/T rs114907564 + CDS Synonymous[Thr590Thr]
1775 .. 1775 T/G rs13173820 + CDS Nonsynonymous[Val592Gly]
1824 .. 1824 C/T rs200022455 + CDS Synonymous[Arg608Arg]
1826 .. 1826 T/C rs200154593 + CDS Nonsynonymous[Leu609Pro]
1862 .. 1862 G/C rs201821221 + CDS Nonsynonymous[Gly621Ala]
1869 .. 1869 C/T rs200931939 + CDS Synonymous[His623His]
1915 .. 1915 G/A rs201391904 + CDS Nonsynonymous[Ala639Thr]
1927 .. 1927 G/A rs200418116 + CDS Nonsynonymous[Gly643Ser]
1983 .. 1983 T/C rs149352680 + CDS Synonymous[Phe661Phe]
2082 .. 2082 C/T rs143630962 + CDS Synonymous[Ser694Ser]
2083 .. 2083 G/A rs114669158 + CDS Nonsynonymous[Ala695Thr]
2086 .. 2086 C/T rs148119281 + CDS Nonsynonymous[Arg696Cys]
2091 .. 2091 C/T rs141873183 + CDS Synonymous[Tyr697Tyr]
2094 .. 2094 A/G rs2233612 + CDS Synonymous[Gly698Gly]
2116 .. 2116 G/A rs116366286 + CDS Nonsynonymous[Val706Met]
2129 .. 2129 G/A rs61749029 + CDS Nonsynonymous[Arg710His]
2156 .. 2156 A/G rs201009079 + CDS Nonsynonymous[Asn719Ser]
2172 .. 2172 C/T rs143362044 + CDS Synonymous[Asn724Asn]
2215 .. 2215 G/A rs200541479 + CDS Nonsynonymous[Gly739Ser]
2231 .. 2231 C/T rs202071188 + CDS Nonsynonymous[Ser744Leu]
2250 .. 2250 G/A rs147534370 + CDS Synonymous[Lys750Lys]
 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