H-InvDB_8.3 released on March 26, 2013. Search by Keyword H-Inv ID (HIT) H-Inv cluster ID (HIX) H-Inv protein ID (HIP) H-Inv gene family/group (HIF) Accession number Chromosome number Chromosome band Definition* Data source ID --- CCDS ID dbSNP ID (rs number) EC number Ensembl ID EntrezGene ID FR ID FR Accession number GO ID GO name* HGNC gene symbol HGNC gene name* InterPro ID InterPro name* OMIM ID OMIM title* Pathway ID Pathway name* RefSeq (gene) ID RefSeq (protein) ID SCOP ID UniProt for Advanced Search

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H-Invitational ID: HIT000051469 Accession number: BC035680 Created date: 26-Mar-2013 Last modified: 20-Apr-2012 Definition: T-cell receptor alpha chain C region;

		Select format Flat file XML file Nucleotide sequence fasta Protein sequence fasta

Transcript original information Accession number BC035680.1 CAGE tag ID NA EST ID NA Clone Number IMAGE:5748161 Experimental resources   NBRC ; HGPD ; Antibody (TRAJ17) ; Catalog (TRAJ17); 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

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

CCGGTGTCGGGAAGCACCAGTGCCCTGAGGAAGGGCCATTTCCAAAAGCC CTGTGCTGACACAGGGTTGCTGGTTCCTCTTCAAGAGCCCACTCTCTGGG GTGGGGCCATATCTCCAGCAGAGGTGGGCTGGAAAGGACCCCCCCAATCC CGCCCGCCGTGAGCTTAGCTGGAGCCATGGCCTCTGCACCCATCTCGATG CTTGCGATGCTCTTCACATTGAGTGGGCTGAGAGCTCAGTCAGTGGCTCA GCCGGAAGATCAGGTCAACGTTGCTGAAGGGAATCCTCTGACTGTGAAAT GCACCTATTCAGTCTCTGGAAACCCTTATCTTTTTTGGTATGTTCAATAC CCCAACCGAGGCCTCCAGTTCCTTCTGAAATACATCACAGGGGATAACCT GGTTAAAGGCAGCTATGGCTTTGAAGCTGAATTTAACAAGAGCCAAACCT CCTTCCACCTGAAGAAACCATCTGCCCTTGTGAGCGACTCCGCTTTGTAC TTCTGTGCTGTGAGAGACGCCAAAGCTGCAGGCAACAAGCTAACTTTTGG AGGAGGAACCAGGGTGCTAGTTAAACCAAATATCCAGAACCCTGACCCTG CCGTGTACCAGCTGAGAGACTCTAAATCCAGTGACAAGTCTGTCTGCCTA TTCACCGATTTTGATTCTCAAACAAATGTGTCACAAAGTAAGGATTCTGA TGTGTATATCACAGACAAAACTGTGCTAGACATGAGGTCTATGGACTTCA AGAGCAACAGTGCTGTGGCCTGGAGCAACAAATCTGACTTTGCATGTGCA AACGCCTTCAACAACAGCATTATTCCAGAAGACACCTTCTTCCCCAGCCC AGAAAGTTCCTGTGATGTCAAGCTGGTCGAGAAAAGCTTTGAAACAGATA CGAACCTAAACTTTCAAAACCTGTCAGTGATTGGGTTCCGAATCCTCCTC CTGAAAGTGGCCGGGTTTAATCTGCTCATGACGCTGCGGCTGTGGTCCAG CTGAGATCTGCAAGATTGTAAGACAGCCTGTGCTCCCTCGCTCCTTCCTC TGCATTGCCCCTCTTCTCCCTCTCCAAACAGAGGGAACTCTCCTACCCCC AAGGAGGTGAAAGCTGCTACCACCTCTGTGCCCCCCCGGCAATGCCACCA ACTGGATCCTACCCGAATTTATGATTAAGATTGCTGAAGAGCTGCCAAAC ACTGCTGCCACCCCCTCTGTTCCCTTATTGCTGCTTGTCACTGCCTGACA TTCACGGCAGAGGCAAGGCTGCTGCAGCCTCCCCTGGCTGTGCACATTCC CTCCTGCTCCCCAGAGACTGCCTCCGCCATCCCACAGATGATGGATCTTC AGTGGGTTCTCTTGGGCTCTAGGTCCTGCAGAATGTTGTGAGGGGTTTAT TTTTTTTTAATAGTGTTCATAAAGAAATACATAGTATTCTTCTTCTCAAG ACGTGGGGGGAAATTATCTCATTATCGAGGCCCTGCTATGCTGTGTATCT GGGCGTGTTGTATGTCCTGCTGCCGATGCCTTCATTAAAATGATTTGGAA GAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Gene structure information

H-Inv cluster ID		HIX0018085
Genomic location	Chromosome	14
	Location	14q11.2
	Position	22191960- 23021097
	Strand	+
Possible duplicated location(s)		NA
Gene structure		7 exon(s)
Database links	RefSeq	NA
	Ensembl	ENST00000390423;  ENST00000390424;  ENST00000390425;  ENST00000390426;  ENST00000390427;  ENST00000390428;  ENST00000390430;  ENST00000390432;  ENST00000390433;  ENST00000390434;  ENST00000390435;  ENST00000390436;  ENST00000390437;  ENST00000390438;  ENST00000390439;  ENST00000390440;  ENST00000390441;  ENST00000390442;  ENST00000390443;  ENST00000390444;  ENST00000390445;  ENST00000390446;  ENST00000390447;  ENST00000390448;  ENST00000390449;  ENST00000390450;  ENST00000390451;  ENST00000390452;  ENST00000390453;  ENST00000390454;  ENST00000390455;  ENST00000390457;  ENST00000390458;  ENST00000390460;  ENST00000390461;  ENST00000390462;  ENST00000390463;  ENST00000390464;  ENST00000390465;  ENST00000390466;  ENST00000390467;  ENST00000390468;  ENST00000390469;  ENST00000390473;  ENST00000390474;  ENST00000390475;  ENST00000390476;  ENST00000390477;  ENST00000390481;  ENST00000390482;  ENST00000390483;  ENST00000390484;  ENST00000390485;  ENST00000390486;  ENST00000390487;  ENST00000390488;  ENST00000390489;  ENST00000390490;  ENST00000390491;  ENST00000390492;  ENST00000390493;  ENST00000390494;  ENST00000390495;  ENST00000390496;  ENST00000390497;  ENST00000390498;  ENST00000390499;  ENST00000390500;  ENST00000390501;  ENST00000390502;  ENST00000390503;  ENST00000390504;  ENST00000390505;  ENST00000390506;  ENST00000390507;  ENST00000390508;  ENST00000390509;  ENST00000390510;  ENST00000390511;  ENST00000390513;  ENST00000390514;  ENST00000390515;  ENST00000390516;  ENST00000390517;  ENST00000390519;  ENST00000390520;  ENST00000390521;  ENST00000390522;  ENST00000390524;  ENST00000390525;  ENST00000390526;  ENST00000390527;  ENST00000390528;  ENST00000390529;  ENST00000390530;  ENST00000390531;  ENST00000390532;  ENST00000390533;  ENST00000390534;  ENST00000390537;  ENST00000442641;  ENST00000446346;  ENST00000478163;  ENST00000480299;  ENST00000537369;  ENST00000542354;
	Entrez Gene	Entrez Gene ID:28738;
	KEGG GENES	KEGG GENES(28738);
	GeneCard	TRAJ17;  *GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links		H-DBAS;  G-integra;  cDNA-genome alignment;

Predicted CDS information HIP ID HIP000033352 Predicted CDS 177..1004;  275[aa];  Orientation:+3;  Codon Adaptation Index (CAI). 0.777

MASAPISMLAMLFTLSGLRAQSVAQPEDQVNVAEGNPLTVKCTYSVSGNP YLFWYVQYPNRGLQFLLKYITGDNLVKGSYGFEAEFNKSQTSFHLKKPSA LVSDSALYFCAVRDAKAAGNKLTFGGGTRVLVKPNIQNPDPAVYQLRDSK SSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWS NKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLS VIGFRILLLKVAGFNLLMTLRLWSS*

Motif information

	a.a. length	InterPro	Name
	119	IPR007110	Immunoglobulin-like [Domain]
	113	IPR013783	Immunoglobulin-like fold [Domain]
	112	IPR013106	Immunoglobulin V-set [Domain]
	107	IPR003599	Immunoglobulin subtype [Domain]
	76	IPR003596	Immunoglobulin V-set, subgroup [Domain]
	89	IPR013783	Immunoglobulin-like fold [Domain]
	84	IPR015370	Domain of unknown function DUF1968 [Domain]

Gene function information

H-Inv ID		HIT000051469
H-Inv cluster ID		HIX0018085
Accession number		BC035680.1
CAGE tag ID		NA
EST ID		NA
Transcript feature		Representative transcript;
Coding potential		Protein coding;
Definition		T-cell receptor alpha chain C region;
Similarity category		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		3873654;  3875483;  12429093;  12796775;  16079912;  19349973;  ALL;
Gene family/group	H-Inv gene family/group ID	HIF0000003
	Gene family/group name	T-cell receptor (TCR).
	Evidence motif (InterPro) ID	NA
Gene symbol/name	HGNC symbol	TRAJ17
	HGNC aliases	NA
	HGNC name	T cell receptor alpha joining 17
	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)	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	ENST00000390423;  ENST00000390424;  ENST00000390425;  ENST00000390426;  ENST00000390427;  ENST00000390428;  ENST00000390430;  ENST00000390432;  ENST00000390433;  ENST00000390434;  ENST00000390435;  ENST00000390436;  ENST00000390437;  ENST00000390438;  ENST00000390439;  ENST00000390440;  ENST00000390441;  ENST00000390442;  ENST00000390443;  ENST00000390444;  ENST00000390445;  ENST00000390446;  ENST00000390447;  ENST00000390448;  ENST00000390449;  ENST00000390450;  ENST00000390451;  ENST00000390452;  ENST00000390453;  ENST00000390454;  ENST00000390455;  ENST00000390457;  ENST00000390458;  ENST00000390460;  ENST00000390461;  ENST00000390462;  ENST00000390463;  ENST00000390464;  ENST00000390465;  ENST00000390466;  ENST00000390467;  ENST00000390468;  ENST00000390469;  ENST00000390473;  ENST00000390474;  ENST00000390475;  ENST00000390476;  ENST00000390477;  ENST00000390481;  ENST00000390482;  ENST00000390483;  ENST00000390484;  ENST00000390485;  ENST00000390486;  ENST00000390487;  ENST00000390488;  ENST00000390489;  ENST00000390490;  ENST00000390491;  ENST00000390492;  ENST00000390493;  ENST00000390494;  ENST00000390495;  ENST00000390496;  ENST00000390497;  ENST00000390498;  ENST00000390499;  ENST00000390500;  ENST00000390501;  ENST00000390502;  ENST00000390503;  ENST00000390504;  ENST00000390505;  ENST00000390506;  ENST00000390507;  ENST00000390508;  ENST00000390509;  ENST00000390510;  ENST00000390511;  ENST00000390513;  ENST00000390514;  ENST00000390515;  ENST00000390516;  ENST00000390517;  ENST00000390519;  ENST00000390520;  ENST00000390521;  ENST00000390522;  ENST00000390524;  ENST00000390525;  ENST00000390526;  ENST00000390527;  ENST00000390528;  ENST00000390529;  ENST00000390530;  ENST00000390531;  ENST00000390532;  ENST00000390533;  ENST00000390534;  ENST00000390537;  ENST00000442641;  ENST00000446346;  ENST00000478163;  ENST00000480299;  ENST00000537369;  ENST00000542354;
	Entrez Gene	Entrez Gene ID:28738;
	KEGG GENES	KEGG GENES(28738);
	GeneCard	TRAJ17;  *GeneCards is provided free to academic non-profit institutions.
	etc	Human-Gene diversity Of Life-style related Diseases;
Curation status		Human curated
Notes		NA
Related H-InvDB links		Gene family;  Similarity Search Tool;  TACT;

fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome.

NA

Subcellular localization information

Last modified:20-Apr-2012

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;  JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP)

Last modified:20-Apr-2012

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

Gene expression information

Last modified:20-Apr-2012

Tissue-specific expression			NA
Probe information	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-ANGEL;  DNAProbeLocator;

Evolutionary information

Last modified:20-Apr-2012

Relationship	Species	Accession number	MGI	Links
Orthology	Monodelphis sp. (Opossum)	AY014504		G-integra
Orthology	Rattus sp. (Rat)	BC092596		G-integra
Orthology	Bos sp. (Cow)	BC147860		G-integra
Orthology	Canis sp. (Dog)	ENSCAFT00000038945		G-integra
Orthology	Pongo sp. (Orangutan)	ENSPPYT00000006662		G-integra
Orthology	Mus sp. (Mouse)	U07662		G-integra
Orthology	Macaca sp. (Macaque)	XM_001098834		G-integra
Orthology	Equus sp. (Horse)	XM_001490440		G-integra
Orthology	Bos sp. (Cow)	XM_601687		G-integra

Phylogenetic tree [View by ATV]	Neighbor-joining (phb)
Related H-InvDB links	Evola;  dN/dS (under constraction);

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information

Single Nucleotide Polymorphism (SNP) and indel  Location Variation dbSNP ID Strand CDS/UTR Translation 130 .. 130 T/C rs35505570 + 5'UTR 135 .. 135 A/C rs61974828 + 5'UTR 147 .. 147 A/G rs926027 + 5'UTR 148 .. 148 T/C rs117249186 + 5'UTR 269 .. 269 C/G rs113553257 + CDS Nonsynonymous[Asn31Lys] 590 .. 590 C/G rs56298757 + CDS Nonsynonymous[Asn138Lys] 799 .. 799 C/G rs111376523 + CDS Nonsynonymous[Ala208Gly] 804 .. 804 G/A rs61740301 + CDS Nonsynonymous[Ala210Thr] 829 .. 829 A/C rs61741618 + CDS Nonsynonymous[Glu218Ala] 830 .. 830 A/G rs1263644 + CDS Synonymous[Glu218Glu] 902 .. 902 G/T rs78619778 + CDS Synonymous[Thr242Thr] 1011 .. 1011 C/A rs74707616 + 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 ^ 1148 -/C rs35249538 + 3'UTR 1163 .. 1163 C/A rs17461 + 3'UTR 1279 ^ 1280 -/C rs33917135 + 3'UTR 1280 ^ 1281 -/C rs34860651 + 3'UTR 1283 .. 1283 C/G rs3699 + 3'UTR 1377 .. 1377 T/C rs3700 + 3'UTR 1378 .. 1378 G/A rs79317848 + 3'UTR 1379 .. 1379 C/G rs3701 + 3'UTR 1428 .. 1428 T/A/C/G rs3702 + 3'UTR 1455 .. 1455 G/C rs116430416 + 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  No data available Database links Human-Gene diversity Of Life-style related Diseases(H-GOLD);  Related H-InvDB links VaryGene;  Repeat Mask Viewer;