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: HIT000435515 Accession number: BC146651 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Protocadherin gamma-A6; PCDH-gamma-A6; Precursor;
 
 

Transcript original information
Accession number BC146651.1
CAGE tag ID NA
EST ID NA
Clone Number MGC:164778 IMAGE:40147340
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 4809[bp] (No. of exon:4)[A:1121 T:1034 G:1246 C:1408]
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: 4757(+) Signal: 4739-4743(+)
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 140753492- 140892539
Strand +
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56109
KEGG GENES KEGG GENES(56109)
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 HIP000031442
Predicted CDS 160..2958;  932[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.759
Database links RefSeq NP_061742
UniProt Q9Y5G7
CCDS CCDS54926

Motif information
ORF

length(932),orf(160:2958)
MAPPQRHPQRSEQVLLLTLLGTLWGAAAAQIRYSIPEELEKGSFVGNIVK
DLGLEPQELAEHGVRIVSRGRMQLFSLNPRNGSLVTAGRIDREELCAQSP
RCLVSFNILVEDKLNLYPVEVEIVDINDNTPRFLKEELEVKILENAAPSS
RFPLMEVYDPDVGMNSLQGFKLSGNSHFSVDVQSEAHGPKYPELVLEGTL
DREGEAVYRLVLTAMDGGDPVRSSVAQILVTVLDVNDNTPMFTQPVYRVS
VPENLPVGTPVLAVTATDQDEGVHGEVTYSFVKITEKISQIFCLNVLTGE
ISTSANLDYEDSSFYELGVEARDGPGLRDRAKVLITILDVNDNVPEVVVT
SGSRTIAESAPPGTVIALFQVFDRDSGLNGLVTCSIPRSLPFELEKSVGN
YYRLVTNAALDREEVFLYNITVTATDKGTPPLSTETIISLNVADTNDNPP
TFPHSSYSVYVLENNPRGASIFSVNALDPDVDQNAQVSYSLAEDTLQGAP
LSSYVSINSDTGILYALRSFDYEQLRDLQLWVTASDSGDPPLSSNVSLSL
FVLDQNDNAPEILYPALPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQ
NAWLSYRLLKASEPGLFSVGLHTGEVRTARALLDRDALKQSLVVAVQDHG
QPPLSATVTLTVAVADRIPDILADLGSLEPSAKPNDSDLTLYLVVAVAAV
SCVFLAFVIVLLALRLQRWHKSRLLQASGGGLASMPGSHFVGVEGVRAFL
QTYSHEVSLTADSRKSHLIFPQPNYADTLINQESYEKSEPLLITQDLLET
KGEPRQLQQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQA
MILASASEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGS
NATLTNAAGKRDGKAPAGGNGNKKKSGKKEKK*
a.a.
length
InterPro Name
length(95), motif(30:124) 95 IPR015919 Cadherin-like [Domain]
length(83), motif(30:112) 83 IPR013164 Cadherin, N-terminal [Domain]
length(101), motif(30:130) 101 IPR002126 Cadherin [Domain]
length(87), motif(45:131) 87 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(108), motif(127:234) 108 IPR015919 Cadherin-like [Domain]
length(109), motif(131:239) 109 IPR002126 Cadherin [Domain]
length(109), motif(134:242) 109 IPR002126 Cadherin [Domain]
length(94), motif(140:233) 94 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(120), motif(230:349) 120 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(92), motif(247:338) 92 IPR002126 Cadherin [Domain]
length(82), motif(264:345) 82 IPR002126 Cadherin [Domain]
length(13), motif(314:326) 13 IPR002126 Cadherin [Domain]
length(20), motif(326:345) 20 IPR002126 Cadherin [Domain]
length(11), motif(335:345) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(340:444) 105 IPR015919 Cadherin-like [Domain]
length(105), motif(344:448) 105 IPR002126 Cadherin [Domain]
length(98), motif(355:452) 98 IPR002126 Cadherin [Domain]
length(88), motif(355:442) 88 IPR002126 Cadherin [Domain]
length(82), motif(369:450) 82 IPR002126 Cadherin [Domain]
length(11), motif(440:450) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(125), motif(441:565) 125 IPR015919 Cadherin-like [Domain]
length(115), motif(449:563) 115 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(111), motif(556:666) 111 IPR015919 Cadherin-like [Domain]
length(104), motif(579:682) 104 IPR002126 Cadherin [Domain]
length(88), motif(579:666) 88 IPR002126 Cadherin [Domain]
length(83), motif(582:664) 83 IPR002126 Cadherin [Domain]
length(79), motif(591:669) 79 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000435515
H-Inv cluster ID Locus viewHIX0005252
Accession number BC146651.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-A6; PCDH-gamma-A6; Precursor;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q9Y5G7)  [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 PCDHGA6
UniProt PCDHGA6
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 HIP000031442
No. of interaction 17
Interaction partner(s) HIP000008344HIP000031320HIP000031320HIP000032747HIP000042725HIP000046840HIP000058821HIP000082042HIP000082159HIP000097730HIP000104226HIP000104226HIP000107876HIP000125556HIP000135268HIP000149098HIP000310114
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56109
KEGG GENES KEGG GENES(56109)
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;  endoplasmic;  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
37 100 1f5aA1 8e-17 20.7 58/118 d.58.16.1
127 234 1edhA2 2e-14 26.8 108/112 b.1.6.1
208 524 2nlzA1 9e-64 10.8 295/533 d.153.1.6
504 666 1o75A3 2e-14 6.9 152/191 b.120.1.1
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
33 .. 33 C/A rs114705983 + 5'UTR
115 .. 115 G/T rs187674758 + 5'UTR
180 .. 180 T/G rs200348921 + CDS Nonsynonymous[His7Gln]
215 .. 215 T/C rs199514730 + CDS Nonsynonymous[Leu19Pro]
351 .. 351 C/A rs3749775 - CDS Synonymous[Val64Val]
436 .. 436 G/A rs200765071 + CDS Nonsynonymous[Glu93Lys]
459 .. 459 G/A rs192911480 + CDS Synonymous[Pro100Pro]
479 .. 479 A/G rs201390749 + CDS Nonsynonymous[Asn107Ser]
636 .. 636 C/A rs185125730 + CDS Nonsynonymous[Asp159Glu]
781 .. 781 T/A rs188037010 + CDS Nonsynonymous[Tyr208Asn]
849 .. 849 A/T rs192855761 + CDS Synonymous[Val230Val]
901 .. 901 C/A rs11575953 + CDS Nonsynonymous[Arg248Ser]
1045 .. 1045 G/A rs200408172 + CDS Nonsynonymous[Val296Ile]
1122 .. 1122 C/T rs183723314 + CDS Synonymous[Ala321Ala]
1123 .. 1123 C/T rs201669950 + CDS Nonsynonymous[Arg322Trp]
1185 .. 1185 T/C rs199796645 + CDS Synonymous[Asp342Asp]
1275 .. 1275 C/G rs188091361 + CDS Nonsynonymous[Phe372Leu]
1339 .. 1339 T/C rs200233213 + CDS Synonymous[Leu394Leu]
1419 .. 1419 C/T rs114810218 + CDS Synonymous[Ile420Ile]
1483 .. 1483 G/A rs192651675 + CDS Nonsynonymous[Val442Met]
1487 .. 1487 C/T rs73265852 + CDS Nonsynonymous[Ala443Val]
1536 .. 1536 C/G rs184685234 + CDS Synonymous[Val459Val]
1731 .. 1731 G/A rs117560542 + CDS Synonymous[Gln524Gln]
1741 .. 1741 C/T rs114223268 + CDS Synonymous[Leu528Leu]
1769 .. 1769 G/C rs112671050 + CDS Nonsynonymous[Ser537Thr]
1843 .. 1843 A/T rs190439419 + CDS Nonsynonymous[Ile562Phe]
1865 .. 1865 C/T rs200873701 + CDS Nonsynonymous[Thr569Ile]
1896 .. 1896 C/T rs62378422 + CDS Synonymous[Pro579Pro]
1913 .. 1913 G/A rs201669321 + CDS Nonsynonymous[Gly585Asp]
2004 .. 2004 A/G rs3749773 - CDS Synonymous[Gly615Gly]
2019 .. 2019 C/T rs111303338 + CDS Synonymous[Gly620Gly]
2043 .. 2043 G/A rs200712802 + CDS Synonymous[Thr628Thr]
2050 .. 2050 G/A rs181747779 + CDS Nonsynonymous[Ala631Thr]
2082 .. 2082 C/A rs11575954 + CDS Nonsynonymous[Ser641Arg]
2085 .. 2085 A/C rs111388524 + CDS Synonymous[Leu642Leu]
2109 .. 2109 C/G rs13154181 + CDS Synonymous[Gly650Gly]
2119 .. 2119 C/T rs201022484 + CDS Nonsynonymous[Leu654Phe]
2137 .. 2137 C/G rs201851177 + CDS Nonsynonymous[Leu660Val]
2170 .. 2170 A/C rs9324847 + CDS Nonsynonymous[Ile671Leu]
2207 .. 2207 A/T rs200974904 + CDS Nonsynonymous[Lys683Ile]
2241 .. 2241 G/A rs181247360 + CDS Synonymous[Val694Val]
2256 .. 2256 G/C rs113596971 + CDS Synonymous[Ala699Ala]
2280 .. 2280 C/A rs185484474 + CDS Nonsynonymous[Phe707Leu]
2286 .. 2286 C/T rs112869528 + CDS Synonymous[Ile709Ile]
2288 .. 2288 T/C rs200049429 + CDS Nonsynonymous[Val710Ala]
2309 .. 2309 A/G rs2159258 + CDS Nonsynonymous[Gln717Arg]
2312 .. 2312 G/T rs202155785 + CDS Nonsynonymous[Arg718Leu]
2342 .. 2342 C/T rs200515281 + CDS Nonsynonymous[Ser728Leu]
2352 .. 2352 C/A rs3749771 - CDS Synonymous[Gly731Gly]
2369 .. 2369 G/C rs189836587 + CDS Nonsynonymous[Gly737Ala]
2376 .. 2376 C/G rs202008607 + CDS Nonsynonymous[His739Gln]
2391 .. 2391 A/C rs182104750 + CDS Nonsynonymous[Glu744Asp]
2410 .. 2410 C/A rs11575955 + CDS Nonsynonymous[Gln751Lys]
2438 .. 2438 C/G rs186469397 + CDS Nonsynonymous[Thr760Ser]
2559 .. 2559 G/T rs139873493 + CDS Synonymous[Thr800Thr]
2579 .. 2579 T/C rs192154001 + CDS Nonsynonymous[Leu807Pro]
2620 .. 2620 G/A rs201391904 + CDS Nonsynonymous[Ala821Thr]
2632 .. 2632 G/A rs200418116 + CDS Nonsynonymous[Gly825Ser]
2688 .. 2688 T/C rs149352680 + CDS Synonymous[Phe843Phe]
2787 .. 2787 C/T rs143630962 + CDS Synonymous[Ser876Ser]
2788 .. 2788 G/A rs114669158 + CDS Nonsynonymous[Ala877Thr]
2791 .. 2791 C/T rs148119281 + CDS Nonsynonymous[Arg878Cys]
2796 .. 2796 C/T rs141873183 + CDS Synonymous[Tyr879Tyr]
2799 .. 2799 A/G rs2233612 + CDS Synonymous[Gly880Gly]
2821 .. 2821 G/A rs116366286 + CDS Nonsynonymous[Val888Met]
2834 .. 2834 G/A rs61749029 + CDS Nonsynonymous[Arg892His]
2861 .. 2861 A/G rs201009079 + CDS Nonsynonymous[Asn901Ser]
2877 .. 2877 C/T rs143362044 + CDS Synonymous[Asn906Asn]
2920 .. 2920 G/A rs200541479 + CDS Nonsynonymous[Gly921Ser]
2936 .. 2936 C/T rs202071188 + CDS Nonsynonymous[Ser926Leu]
2955 .. 2955 G/A rs147534370 + CDS Synonymous[Lys932Lys]
2987 .. 2987 C/T rs201024828 + 3'UTR
2988 .. 2988 G/A rs2233613 + 3'UTR
3093 .. 3093 G/A rs76613492 + 3'UTR
3149 .. 3149 T/C rs115159796 + 3'UTR
3159 .. 3159 C/A rs191106767 + 3'UTR
3395 .. 3395 C/A rs146235929 + 3'UTR
3413 .. 3413 G/C rs4912608 + 3'UTR
3488 .. 3488 T/G rs148447880 + 3'UTR
3650 .. 3650 G/A rs142624814 + 3'UTR
3671 .. 3671 T/C rs113814137 + 3'UTR
3677 .. 3677 C/T rs150999050 + 3'UTR
3684 .. 3684 T/G rs187622252 + 3'UTR
3873 .. 3873 A/G rs192947391 + 3'UTR
3956 .. 3956 T/C rs140884268 + 3'UTR
3979 .. 3979 G/A rs111365449 + 3'UTR
4170 .. 4170 A/G rs78180647 + 3'UTR
4238 .. 4238 G/A rs185198109 + 3'UTR
4331 .. 4331 C/T rs147780926 + 3'UTR
4624 .. 4624 C/T rs141207714 + 3'UTR
4643 .. 4643 G/T rs189734474 + 3'UTR
4699 .. 4699 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