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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000340211 Accession number: BC112082 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Protocadherin gamma-A1; PCDH-gamma-A1; Precursor;
 
 

Transcript original information
Accession number BC112082.1
CAGE tag ID NA
EST ID NA
Clone Number MGC:138287 IMAGE:8327550
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ;
Sequence data provider NA
Annotation project NA
Length of cDNA 2616[bp] (No. of exon:1)[A:659 T:598 G:643 C:716]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Lung, PCR rescued clones
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) NA
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0216337
Genomic location  G-integra Help Chromosome 5
Location 5q31.3
Position 140710204- 140712819
Strand +
Possible duplicated location(s) NA
Gene structure 1 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56114
KEGG GENES KEGG GENES(56114)
GeneCard NA *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 HIP000157503
Predicted CDS 49..2520;  823[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.74

Motif information
ORF

length(823),orf(49:2520)
MKIQKKLTGCSRLMLLCLSLELLLEAGAGNIHYSVPEETDKGSFVGNIAK
DLGLQPQELADGGVRIVSRGRMPLFALNPRSGSLITARRIDREELCAQSM
PCLVSFNILVEDKMKLFPVEVEIIDINDNTPQFQLEELEFKMNEITTPGT
RISLPFGQDLDVGMNSLQSYQLSSNPHFSLDVQQGADGPQHPEMVLQSPL
DREEEAVHHLILTASDGGEPVRSGTLRIYIQVVDANDNPPAFTQAQYHIN
VPENVPLGTQLLMVNATDPDEGANGEVTYSFHNVDHRVAQIFRLDSYTGE
ISNKEPLDFEEYKMYSMEVQAQDGAGLMAKVKVLIKVLDVNDNAPEVTIT
SVTTAVPENFPPGTIIALISVHDQDSGDNGYTTCFIPGNLPFKLEKLVDN
YYRLVTERTLDRELISGYNITITAIDQGTPALSTETHISLLVTDINDNSP
VFHQDSYSAYIPENNPRGASIFSVRAHDLDSNENAQITYSLIEDTIQGAP
LSAYLSINSDTGVLYALRSFDYEQFRDMQLKVMARDSGDPPLSSNVSLSL
FLLDQNDNAPEILYPALPTDGSTGVELAPLSAEPGYLVTKVVAVDRDSGQ
NAWLSYRLLKASEPGLFSVGLHTGEVRTARALLDRDALKQSLVVAVQDHG
QPPLSATVTLTVAVADRISDILADLGSLEPSAKPNDSDLTLYLVVAAAAV
SCVFLAFVIVLLAHRLRRWHKSRLLQASGGGLASMPGSHFVGVDGVRAFL
QTYSHEVSLTADSRKSHLIFPQPNYADTLISQESCEKKGFLSAPQSLLED
KKEPFSQVNFCDECISYLEKNNS*
a.a.
length
InterPro Name
length(83), motif(30:112) 83 IPR013164 Cadherin, N-terminal [Domain]
length(75), motif(31:105) 75 IPR015919 Cadherin-like [Domain]
length(93), motif(31:123) 93 IPR002126 Cadherin [Domain]
length(101), motif(31:131) 101 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(116), motif(124:239) 116 IPR002126 Cadherin [Domain]
length(108), motif(127:234) 108 IPR015919 Cadherin-like [Domain]
length(109), motif(134:242) 109 IPR002126 Cadherin [Domain]
length(93), motif(140:232) 93 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(104), motif(236:339) 104 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(105), motif(348:452) 105 IPR002126 Cadherin [Domain]
length(89), motif(354:442) 89 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(93), motif(457:549) 93 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(102), motif(581:682) 102 IPR002126 Cadherin [Domain]
length(86), motif(581:666) 86 IPR002126 Cadherin [Domain]
length(82), motif(583:664) 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 HIT000340211
H-Inv cluster ID Locus viewHIX0216337
Accession number BC112082.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Similar to Protocadherin gamma-A1; PCDH-gamma-A1; Precursor;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (Q9Y5H4)  [Identity/coverage = 97.77%/86.68%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 10380929ALL
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 NA
HGNC aliases NA
HGNC name NA
DDBJ PCDHGA1
UniProt PCDHGA1
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 HIP000157503
No. of interaction 2
Interaction partner(s) HIP000176774HIP000247062
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56114
KEGG GENES KEGG GENES(56114)
GeneCard NA *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
33 99 1f5aA1 6e-18 21.3 61/118 d.58.16.1
129 524 2nlzA1 3e-67 10.7 374/533 d.153.1.6
504 666 1o75A3 3e-14 7.5 152/191 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 AGhsA110108; 
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 2832537;  2832538;  2832539;  2832540;  2832541;  2832542;  2878651; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_23_P422044; 
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
61 .. 61 A/G rs201710711 + CDS Nonsynonymous[Lys5Glu]
109 .. 109 G/C rs141990511 + CDS Nonsynonymous[Glu21Gln]
135 .. 135 G/A rs146187959 + CDS Synonymous[Gly29Gly]
201 .. 201 C/- rs35733112 + CDS
210 .. 210 G/A rs139081093 + CDS Synonymous[Leu54Leu]
219 .. 219 G/A rs115490425 + CDS Synonymous[Gln57Gln]
225 .. 225 G/A rs199546998 + CDS Synonymous[Leu59Leu]
258 .. 258 T/C rs72806843 + CDS Synonymous[Gly70Gly]
286 .. 286 A/G rs139589644 + CDS Nonsynonymous[Arg80Gly]
340 .. 340 C/G rs149721215 + CDS Nonsynonymous[Gln98Glu]
373 .. 373 C/T rs145540103 + CDS Nonsynonymous[Leu109Phe]
481 .. 481 A/G rs201568844 + CDS Nonsynonymous[Ile145Val]
502 .. 502 A/G rs2472647 - CDS Nonsynonymous[Ile152Val]
557 .. 557 A/C rs147001042 + CDS Nonsynonymous[Tyr170Ser]
575 .. 575 C/T rs147674827 + CDS Nonsynonymous[Pro176Leu]
607 .. 607 G/A rs76571170 + CDS Nonsynonymous[Asp187Asn]
629 .. 629 T/C rs146641474 + CDS Nonsynonymous[Met194Thr]
691 .. 691 T/G rs116468502 + CDS Nonsynonymous[Ser215Ala]
713 .. 713 G/A rs139152286 + CDS Nonsynonymous[Arg222His]
736 .. 736 A/G rs115370042 + CDS Nonsynonymous[Ile230Val]
791 .. 791 A/C rs58894014 + CDS Nonsynonymous[His248Pro]
805 .. 805 G/A rs140226913 + CDS Nonsynonymous[Glu253Lys]
854 .. 854 C/T rs138254459 + CDS Nonsynonymous[Pro269Leu]
856 .. 856 G/A rs149650270 + CDS Nonsynonymous[Asp270Asn]
865 .. 865 G/A rs146145941 + CDS Nonsynonymous[Ala273Thr]
882 .. 882 G/A rs115965295 + CDS Synonymous[Thr278Thr]
888 .. 888 C/A rs150032730 + CDS Synonymous[Ser280Ser]
894 .. 894 C/G rs17097185 + CDS Nonsynonymous[His282Gln]
925 .. 925 C/T rs145926133 + CDS Nonsynonymous[Arg293Cys]
975 .. 975 C/T rs148638556 + CDS Synonymous[Phe309Phe]
976 .. 976 G/A rs201338329 + CDS Nonsynonymous[Glu310Lys]
1003 .. 1003 G/C rs142099106 + CDS Nonsynonymous[Val319Leu]
1056 .. 1056 A/G rs116275017 + CDS Synonymous[Lys336Lys]
1066 .. 1066 G/A rs151199533 + CDS Nonsynonymous[Val340Ile]
1150 .. 1150 C/G rs139139120 + CDS Nonsynonymous[Leu368Val]
1159 .. 1159 G/A rs114855745 + CDS Nonsynonymous[Val371Met]
1176 .. 1176 A/T rs115219843 + CDS Synonymous[Ser376Ser]
1243 .. 1243 G/A rs116715037 + CDS Nonsynonymous[Asp399Asn]
1256 .. 1256 G/A rs11575961 + CDS Nonsynonymous[Arg403His]
1344 .. 1344 A/G rs114498220 + CDS Synonymous[Leu432Leu]
1392 .. 1392 C/T rs111327215 + CDS Synonymous[Asn448Asn]
1427 .. 1427 A/G rs147638996 + CDS Nonsynonymous[Tyr460Cys]
1528 .. 1528 G/A rs142231440 + CDS Nonsynonymous[Asp494Asn]
1529 .. 1529 A/G rs146367786 + CDS Nonsynonymous[Asp494Gly]
1535 .. 1535 T/C rs145695495 + CDS Nonsynonymous[Ile496Thr]
1571 .. 1571 A/G rs148959678 + CDS Nonsynonymous[Asn508Ser]
1583 .. 1583 G/A rs116469894 + CDS Nonsynonymous[Gly512Glu]
1650 .. 1650 G/A rs17097187 + CDS Synonymous[Ala534Ala]
1684 .. 1684 G/C rs188815514 + CDS Nonsynonymous[Val546Leu]
1704 .. 1704 G/A rs115095833 + CDS Synonymous[Leu552Leu]
1711 .. 1711 C/T rs202093782 + CDS AA-STOP[Gln555*]
1721 .. 1721 A/G rs142949915 + CDS Nonsynonymous[Asn558Ser]
1728 .. 1728 C/G rs200405477 + CDS Synonymous[Pro560Pro]
1751 .. 1751 C/G rs116679801 + CDS Nonsynonymous[Pro568Arg]
1768 .. 1768 G/C rs115926650 + CDS Nonsynonymous[Gly574Arg]
1797 .. 1797 G/T rs192894542 + CDS Nonsynonymous[Glu583Asp]
1876 .. 1876 A/C rs142197826 + CDS Nonsynonymous[Lys610Gln]
1914 .. 1914 C/G rs145945754 + CDS Nonsynonymous[His622Gln]
1971 .. 1971 T/C rs7736087 + CDS Synonymous[Ser641Ser]
1995 .. 1995 C/T rs138362456 + CDS Synonymous[His649His]
2007 .. 2007 G/T rs62378403 + CDS Synonymous[Pro653Pro]
2007 .. 2007 G/T rs112347072 + CDS Synonymous[Pro653Pro]
2008 .. 2008 C/T rs149280390 + CDS Nonsynonymous[Leu654Phe]
2020 .. 2020 G/A rs144494457 + CDS Nonsynonymous[Val658Ile]
2040 .. 2040 G/A rs201668090 + CDS Synonymous[Val664Val]
2053 .. 2053 T/C rs148466345 + CDS Nonsynonymous[Ser669Pro]
2067 .. 2067 C/T rs145246231 + CDS Synonymous[Ala673Ala]
2096 .. 2096 A/T rs62378404 + CDS Nonsynonymous[Lys683Ile]
2138 .. 2138 C/T rs140634036 + CDS Nonsynonymous[Ala697Val]
2170 .. 2170 G/C rs144483624 + CDS Nonsynonymous[Val708Leu]
2172 .. 2172 C/A rs151257732 + CDS Synonymous[Val708Val]
2179 .. 2179 C/T rs199711240 + CDS Synonymous[Leu711Leu]
2217 .. 2217 T/C rs140436541 + CDS Synonymous[Arg723Arg]
2219 .. 2219 T/C rs150021187 + CDS Nonsynonymous[Leu724Pro]
2223 .. 2223 A/G rs145241441 + CDS Synonymous[Leu725Leu]
2248 .. 2248 A/G rs141275772 + CDS Nonsynonymous[Ser734Gly]
2257 .. 2257 G/A rs113017417 + CDS Nonsynonymous[Gly737Ser]
2258 .. 2258 G/T rs200683011 + CDS Nonsynonymous[Gly737Val]
2365 .. 2365 C/T rs200655156 + CDS Nonsynonymous[Pro773Ser]
2380 .. 2380 A/G rs57846288 + CDS Nonsynonymous[Thr778Ala]
2382 .. 2382 A/G rs116015775 + CDS Synonymous[Thr778Thr]
2383 .. 2383 C/T rs11575968 + CDS Nonsynonymous[Leu779Phe]
2398 .. 2398 A/G rs111873293 + CDS Nonsynonymous[Ser784Gly]
2413 .. 2413 G/A rs143810163 + CDS Nonsynonymous[Gly789Ser]
2450 .. 2450 A/G rs147043551 + CDS Nonsynonymous[Lys801Arg]
2492 .. 2492 T/C rs115971518 + CDS Nonsynonymous[Ile815Thr]
2495 .. 2495 G/A rs114133466 + CDS Nonsynonymous[Ser816Asn]
2547 .. 2547 C/G rs141913516 + 3'UTR
2569 .. 2569 A/G rs188101907 + 3'UTR
2609 .. 2609 A/G rs182019371 + 3'UTR
2610 .. 2610 C/A rs185548582 + 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
Type Start End Strand
MamRTE1 1293 1341 +
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD)
Related H-InvDB links VaryGeneVaryGene Repeat mask viewerRepeat Mask Viewer