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H-Invitational ID: HIT000051469 Accession number: BC035680 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: T-cell receptor alpha chain C region;
 
 

Transcript original information
Accession number BC035680.1
CAGE tag ID NA
EST ID NA
Clone Number IMAGE:5748161
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ;
Sequence data provider Provider:MGC/NCI
Annotation project H-Invitational FLcDNA
Length of cDNA 1590[bp] (No. of exon:7)[A:405 T:397 G:362 C:426]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Pancreas, Spleen, adult pooled
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 1555(+) Signal: 1534-1538(+)
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 HIX0018085
Genomic location  G-integra Help Chromosome 14
Location 14q11.2
Position 22191960- 23021097
Strand +
Possible duplicated location(s) NA
Gene structure 7 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:28738
KEGG GENES KEGG GENES(28738)
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 HIP000033352
Predicted CDS 177..1004;  275[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.777

Motif information
ORF

length(275),orf(177:1004)
MASAPISMLAMLFTLSGLRAQSVAQPEDQVNVAEGNPLTVKCTYSVSGNP
YLFWYVQYPNRGLQFLLKYITGDNLVKGSYGFEAEFNKSQTSFHLKKPSA
LVSDSALYFCAVRDAKAAGNKLTFGGGTRVLVKPNIQNPDPAVYQLRDSK
SSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLS
VIGFRILLLKVAGFNLLMTLRLWSS*
a.a.
length
InterPro Name
length(119), motif(5:123) 119 IPR007110 Immunoglobulin-like domain [Domain]
length(114), motif(21:134) 114 IPR013783 Immunoglobulin-like fold [Domain]
length(112), motif(21:132) 112 IPR013106 Immunoglobulin V-set domain [Domain]
length(89), motif(135:223) 89 IPR013783 Immunoglobulin-like fold [Domain]
length(84), motif(141:224) 84 IPR015370 Domain of unknown function DUF1968 [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000051469
H-Inv cluster ID Locus viewHIX0018085
Accession number BC035680.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript; 
Coding potential  Help Protein coding; 
Definition T-cell receptor alpha chain C region;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (P01848)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 3873654387548312429093127967751607991219349973ALL
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 NA
UniProt TRAC
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 HIP000033352
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:28738
KEGG GENES KEGG GENES(28738)
GeneCard NA *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Human curated
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 protein binding (GO:0005515); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT extracellular;  plasma membrane;  peroxisome;  Other; 
Target P signal peptide
SOSUI soluble protein
TMHMM soluble 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
27 134 1q8mA 2e-16 17.9 106/121 b.1.1.1
136 221 1bd2D2 3e-27 100.0 79/79 b.1.1.2
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 AGhsB031110;  AGhsC081622; 
Affymetrix
GeneChip
HG-Focus NA
HG-U133 209670_at;  209671_x_at;  210972_x_at;  211902_x_at;  215524_x_at; 
HG-U133A 209670_at;  209671_x_at;  210972_x_at;  211902_x_at;  215524_x_at; 
HG-U133A_2 209670_at;  209671_x_at;  210972_x_at;  211902_x_at;  215524_x_at; 
HG-U133B NA
HG-U133_Plus_2 209670_at;  209671_x_at;  210972_x_at;  211902_x_at;  215524_x_at; 
HG-U95 1106_s_at;  31710_at;  432_s_at; 
HG-U95A 1106_s_at;  31710_at;  432_s_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 3528184;  3528185;  3528186;  3528573;  3528596;  3528597;  3528600;  3528601;  3528602;  3528603;  3528604;  3556569; 
HuGeneFL K02777_s_at;  M12959_s_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P258504;  A_23_P258798; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P258504; 
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

Evolutionary information  Evola Help Last modified:27-May-2015
Relationship Species Accession number MGI Links
Orthology Monodelphis sp. (Opossum) AY014504 G-integraG-integra
Orthology Rattus sp. (Rat) BC092596 G-integraG-integra
Orthology Bos sp. (Cow) BC147860 G-integraG-integra
Orthology Canis sp. (Dog) ENSCAFT00000038945 G-integraG-integra
Orthology Pongo sp. (Orangutan) ENSPPYT00000006662 G-integraG-integra
Orthology Mus sp. (Mouse) U07662 G-integraG-integra
Orthology Macaca sp. (Macaque) XM_001098834 G-integraG-integra
Orthology Equus sp. (Horse) XM_001490440 G-integraG-integra
Orthology Bos sp. (Cow) XM_601687 G-integraG-integra
Phylogenetic tree [View by ATV]
Neighbor-joining (phb) 
Related H-InvDB links EvolaEvoladN/dS (under constraction); 

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
9 .. 9 G/A rs191961603 + 5'UTR
79 .. 79 C/G rs144208720 + 5'UTR
130 .. 130 T/C rs35505570 + 5'UTR
135 .. 135 A/C rs61974828 + 5'UTR
147 .. 147 A/G rs926027 + 5'UTR
245 .. 245 G/A rs182837293 + CDS Synonymous[Val23Val]
269 .. 269 C/G rs113553257 + CDS Nonsynonymous[Asn31Lys]
532 .. 532 G/T rs148590887 + CDS Nonsynonymous[Gly119Val]
590 .. 590 C/G rs56298757 + CDS Nonsynonymous[Asn138Lys]
777 .. 777 A/G rs184088135 + CDS Nonsynonymous[Asn201Asp]
791 .. 791 T/A rs188818338 + CDS Nonsynonymous[Phe205Leu]
793 .. 793 C/T rs138496993 + CDS Nonsynonymous[Ala206Val]
799 .. 799 C/G rs111376523 + CDS Nonsynonymous[Ala208Gly]
804 .. 804 G/A rs61740301 + CDS Nonsynonymous[Ala210Thr]
812 .. 812 C/T rs181336928 + CDS Synonymous[Asn212Asn]
819 .. 819 A/G rs141035173 + CDS Nonsynonymous[Ile215Val]
829 .. 829 A/C rs61741618 + CDS Nonsynonymous[Glu218Ala]
830 .. 830 A/G rs1263644 + CDS Synonymous[Glu218Glu]
902 .. 902 G/T rs78619778 + CDS Synonymous[Thr242Thr]
993 .. 993 T/C rs201133432 + CDS Nonsynonymous[Trp273Arg]
1034 .. 1034 T/C rs202179565 + 3'UTR
1072 .. 1072 C/T rs140338675 + 3'UTR
1087 .. 1087 A/G rs45512705 + 3'UTR
1094 .. 1094 T/C rs15795 + 3'UTR
1127 .. 1127 T/C rs112310271 + 3'UTR
1146 ^ 1147 -/C rs11462449 + 3'UTR
1147 .. 1147 A/C rs201208032 + 3'UTR
1147 ^ 1148 -/A/C rs35249538 + 3'UTR
1148 .. 1148 C/A rs201672662 - 3'UTR
1163 .. 1163 C/A rs17461 + 3'UTR
1279 ^ 1280 -/C rs33917135 + 3'UTR
1280 .. 1280 T/C rs200455004 + 3'UTR
1283 .. 1283 C/G rs3699 + 3'UTR
1296 .. 1296 A/T rs144196489 + 3'UTR
1300 .. 1300 C/T rs151169555 + 3'UTR
1377 .. 1377 T/C rs3700 + 3'UTR
1378 .. 1378 G/A rs79317848 + 3'UTR
1379 .. 1379 C/G rs3701 + 3'UTR
1405 .. 1405 T/C rs139070275 + 3'UTR
1428 .. 1428 T/A/C/G rs3702 + 3'UTR
1453 .. 1453 G/A rs200432327 + 3'UTR
1455 .. 1455 G/C rs116430416 + 3'UTR
1460 .. 1460 G/A rs149828865 + 3'UTR
1476 .. 1476 C/T rs201193295 + 3'UTR
1497 .. 1497 A/G rs9125 + 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