H-InvDB x AHG DB
Transcript view
H-InvDB_9.0 released on May 27, 2015.
Search by for Advanced Search
Home Quick guide Navi BLAST Site map Download Contact us Help
H-Invitational ID: HIT000071813 Accession number: AF152509 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Protocadherin gamma-A2; PCDH-gamma-A2; Precursor;
 
 

Transcript original information
Accession number AF152509.1
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 2712[bp] (No. of exon:5)[A:637 T:545 G:730 C:800]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type NA
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature N-truncated
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 140723601- 140890750
Strand +
Possible duplicated location(s) NA
Gene structure 5 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene NA
KEGG GENES NA
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 HIP000183290
Predicted CDS 213..2702;  829[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.769

Motif information
ORF

length(829),orf(213:2702)
DAAFLSESAKRQLGHRGEDRPGGALRSDPAVSEELEIKIGELTVPGTRFP
IKTAFDPDVGINSLQNYKLSPNDYFSLAVNSVSEGAKYPELVLERALDRE
KKEIHQLVLVASDGGDPVHSGNLHIQVIVLDANDNPPMFTQPEYRVSVWE
NVPVGTRLLTVNATDPDEGFNAQVSYILDKMPGKIAEIFHLNSVSGEVSI
LKSLDYEDAMFYEIKIEAQDGPGLLSRANILVTVLDVNDNAPEITITSLT
SSVPEEGTVGREIALIDVHDRDSGQNGQVEVFVLGNLPFKLEKSIDQYYR
LVTATSLDREQISEYNISLRASDGGSPPLSTETHITLHVIDINDNPPTFP
HLSYSAYIPENNPRGASIFSVTAQDPDSNNNARITYALTEDTLQGAPLSS
FVSINSNTGVLYALRSFDYEQFRDLKLLVTASDSGNPPLSSIVSLNLFVL
DQNDNAPEILYPALPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAW
LSYRLLKASEPGLFSVGLHTGEVRTARALLDRDALKQSLVVAVQDHGQPP
LSATVTLTVAVADRIPDILADLGSLEPSAKPNDSDLTLYLVVAVAAVSCV
FLAFVIVLLALRLRRWHKSRLLQASGGGLASTPGSHFVGVDGVRAFLQTY
SHEVSLTADSRKSHLIFPQPNYADTLISQESCEKSEPLLITQDLLEMKGD
SNLLQQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMIL
ASASEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNAT
LTNAAGKRDGKAPAGGNGNKKKSGKKEKK*
a.a.
length
InterPro Name
length(109), motif(31:139) 109 IPR002126 Cadherin [Domain]
length(104), motif(33:136) 104 IPR002126 Cadherin [Domain]
length(97), motif(35:131) 97 IPR015919 Cadherin-like [Domain]
length(86), motif(52:137) 86 IPR002126 Cadherin [Domain]
length(11), motif(127:137) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(104), motif(134:237) 104 IPR015919 Cadherin-like [Domain]
length(104), motif(137:240) 104 IPR002126 Cadherin [Domain]
length(30), motif(139:168) 30 IPR002126 Cadherin [Domain]
length(105), motif(140:244) 105 IPR002126 Cadherin [Domain]
length(92), motif(144:235) 92 IPR002126 Cadherin [Domain]
length(82), motif(161:242) 82 IPR002126 Cadherin [Domain]
length(13), motif(211:223) 13 IPR002126 Cadherin [Domain]
length(20), motif(223:242) 20 IPR002126 Cadherin [Domain]
length(11), motif(232:242) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(237:341) 105 IPR015919 Cadherin-like [Domain]
length(104), motif(241:344) 104 IPR002126 Cadherin [Domain]
length(105), motif(245:349) 105 IPR002126 Cadherin [Domain]
length(88), motif(252:339) 88 IPR002126 Cadherin [Domain]
length(82), motif(266:347) 82 IPR002126 Cadherin [Domain]
length(11), motif(337:347) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(125), motif(338:462) 125 IPR015919 Cadherin-like [Domain]
length(116), motif(345:460) 116 IPR002126 Cadherin [Domain]
length(14), motif(347:360) 14 IPR002126 Cadherin [Domain]
length(110), motif(350:459) 110 IPR002126 Cadherin [Domain]
length(96), motif(354:449) 96 IPR002126 Cadherin [Domain]
length(87), motif(371:457) 87 IPR002126 Cadherin [Domain]
length(27), motif(407:433) 27 IPR002126 Cadherin [Domain]
length(18), motif(441:458) 18 IPR002126 Cadherin [Domain]
length(11), motif(447:457) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(111), motif(453:563) 111 IPR015919 Cadherin-like [Domain]
length(88), motif(476:563) 88 IPR002126 Cadherin [Domain]
length(104), motif(476:579) 104 IPR002126 Cadherin [Domain]
length(83), motif(479:561) 83 IPR002126 Cadherin [Domain]
length(79), motif(488:566) 79 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000071813
H-Inv cluster ID Locus viewHIX0005252
Accession number AF152509.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Similar to Protocadherin gamma-A2; PCDH-gamma-A2; Precursor;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (Q5DRB8)  [Identity/coverage = 79.599%/99.68%] to Pan troglodytes (Chimpanzee). protein.
Experimental evidence Protein evidence
PubMed ID 1574405216136131ALL
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 NA
UniProt PCDHGA2
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 HIP000183290
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 NA
KEGG GENES NA
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 cytosol;  mitochondria;  nuclear;  Other; 
Target P Other
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
2 284 2nlzA1 2e-53 12.6 261/533 d.153.1.6
344 427 1edhA1 4e-14 14.6 83/99 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 AGhsA110121; 
Affymetrix
GeneChip
HG-Focus 211875_x_at;  216343_at; 
HG-U133 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at;  216352_x_at; 
HG-U133A 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at;  216352_x_at; 
HG-U133A_2 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at;  216352_x_at; 
HG-U133B NA
HG-U133_Plus_2 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_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 2832553;  2832555;  2832751;  2832754;  2832758;  2832759;  2832760;  2832761;  2878647;  2878651; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_23_P422044;  A_24_P334529; 
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
13 .. 13 C/T rs76843294 + 5'UTR
57 .. 57 C/G rs200693710 + 5'UTR
72 .. 72 C/A rs199763392 + 5'UTR
118 .. 118 G/C rs76939403 + 5'UTR
183 .. 183 G/A rs199728541 + 5'UTR
185 .. 185 G/A rs181165081 + 5'UTR
220 .. 220 C/G rs200564331 + CDS Nonsynonymous[Ala3Gly]
235 .. 235 C/T rs11575947 + CDS Nonsynonymous[Ser8Phe]
243 .. 243 C/T rs143610564 + CDS Nonsynonymous[Arg11Trp]
363 .. 363 A/C rs11575948 + CDS Nonsynonymous[Ile51Leu]
427 .. 427 A/G rs147973403 + CDS Nonsynonymous[Asn72Ser]
437 .. 437 C/T rs182334334 + CDS Synonymous[Phe75Phe]
464 .. 464 G/A rs112672535 + CDS Synonymous[Glu84Glu]
467 .. 467 G/A rs199666918 + CDS Synonymous[Gly85Gly]
562 .. 562 C/G rs141617509 + CDS Nonsynonymous[Pro117Arg]
665 .. 665 C/A rs200798114 + CDS Nonsynonymous[Asn151Lys]
844 .. 844 T/C rs150518799 + CDS Nonsynonymous[Phe211Ser]
894 .. 894 G/T rs72790006 + CDS Nonsynonymous[Ala228Ser]
907 .. 907 T/C rs199985204 + CDS Nonsynonymous[Val232Ala]
937 .. 937 C/T rs199942946 + CDS Nonsynonymous[Pro242Leu]
952 .. 952 C/T rs200905776 + CDS Nonsynonymous[Thr247Met]
1103 .. 1103 A/G rs202138177 + CDS Synonymous[Gln297Gln]
1182 .. 1182 G/A rs186274609 + CDS Nonsynonymous[Gly324Arg]
1191 .. 1191 C/G rs200111367 + CDS Nonsynonymous[Pro327Ala]
1199 .. 1199 G/C rs7730183 + CDS Synonymous[Leu329Leu]
1220 .. 1220 C/G rs201216963 + CDS Synonymous[Thr336Thr]
1293 .. 1293 A/G rs190743421 + CDS Nonsynonymous[Asn361Asp]
1314 .. 1314 A/G rs200227313 + CDS Nonsynonymous[Ile368Val]
1336 .. 1336 A/T rs200604016 + CDS Nonsynonymous[Asp375Val]
1349 .. 1349 C/T rs181597586 + CDS Synonymous[Asn379Asn]
1521 .. 1521 C/T rs202221760 + CDS Nonsynonymous[Pro437Ser]
1544 .. 1544 G/T rs2879225 + CDS Synonymous[Ser444Ser]
1553 .. 1553 G/A rs2879226 + CDS Synonymous[Leu447Leu]
1557 .. 1557 G/C rs2879227 + CDS Nonsynonymous[Val449Leu]
1577 .. 1577 C/T rs200612120 + CDS Synonymous[Asn455Asn]
1599 .. 1599 G/T rs200275256 + CDS Nonsynonymous[Ala463Ser]
1602 .. 1602 C/T rs201819603 + CDS Nonsynonymous[Leu464Phe]
1640 .. 1640 T/C rs3749774 - CDS Synonymous[Pro476Pro]
1642 .. 1642 G/T rs4042102 + CDS Nonsynonymous[Arg477Leu]
1666 .. 1666 T/C rs199546235 + CDS Nonsynonymous[Val485Ala]
1718 .. 1718 C/T rs200129248 + CDS Synonymous[Ser502Ser]
1740 .. 1740 G/A rs201026497 + CDS Nonsynonymous[Glu510Lys]
1780 .. 1780 T/A rs200807803 + CDS Nonsynonymous[Val523Glu]
1782 .. 1782 C/A rs62378406 + CDS Nonsynonymous[Arg524Ser]
1784 .. 1784 C/T rs199541335 + CDS Synonymous[Arg524Arg]
1826 .. 1826 C/T rs112486508 + CDS Synonymous[Ser538Ser]
1826 .. 1826 C/T rs7736087 + CDS Synonymous[Ser538Ser]
1839 .. 1839 G/A rs61749030 + CDS Nonsynonymous[Val543Ile]
1862 .. 1862 T/G rs112347072 + CDS Synonymous[Pro550Pro]
1881 .. 1881 C/G rs201663850 + CDS Nonsynonymous[Leu557Val]
1885 .. 1885 C/T rs200367564 + CDS Nonsynonymous[Thr558Ile]
1938 .. 1938 G/A rs201885897 + CDS Nonsynonymous[Glu576Lys]
1951 .. 1951 A/T rs200571439 + CDS Nonsynonymous[Lys580Ile]
2014 ^ 2015 -/GA rs201108847 + CDS
2028 .. 2028 A/T rs200127587 + CDS Nonsynonymous[Ile606Phe]
2111 ^ 2112 -/G rs35104607 + CDS
2131 .. 2131 T/C rs7736541 + CDS Nonsynonymous[Val640Ala]
2143 .. 2143 G/A rs202194695 + CDS Nonsynonymous[Arg644Gln]
2161 .. 2161 A/G rs10069396 + CDS Nonsynonymous[Tyr650Cys]
2226 .. 2226 T/C rs147497475 + CDS Nonsynonymous[Tyr672His]
2266 .. 2266 G/A rs201078369 + CDS Nonsynonymous[Ser685Asn]
2364 .. 2364 G/A rs201391904 + CDS Nonsynonymous[Ala718Thr]
2376 .. 2376 G/A rs200418116 + CDS Nonsynonymous[Gly722Ser]
2432 .. 2432 T/C rs149352680 + CDS Synonymous[Phe740Phe]
2531 .. 2531 C/T rs143630962 + CDS Synonymous[Ser773Ser]
2532 .. 2532 G/A rs114669158 + CDS Nonsynonymous[Ala774Thr]
2535 .. 2535 C/T rs148119281 + CDS Nonsynonymous[Arg775Cys]
2540 .. 2540 C/T rs141873183 + CDS Synonymous[Tyr776Tyr]
2543 .. 2543 A/G rs2233612 + CDS Synonymous[Gly777Gly]
2565 .. 2565 G/A rs116366286 + CDS Nonsynonymous[Val785Met]
2578 .. 2578 G/A rs61749029 + CDS Nonsynonymous[Arg789His]
2605 .. 2605 A/G rs201009079 + CDS Nonsynonymous[Asn798Ser]
2621 .. 2621 C/T rs143362044 + CDS Synonymous[Asn803Asn]
2664 .. 2664 G/A rs200541479 + CDS Nonsynonymous[Gly818Ser]
2680 .. 2680 C/T rs202071188 + CDS Nonsynonymous[Ser823Leu]
2699 .. 2699 G/A rs147534370 + CDS Synonymous[Lys829Lys]
 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