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H-Invitational ID: HIT000042638 Accession number: AK122765 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Transcription factor 4; TCF-4; Class B basic helix-loop-helix protein 19; bHLHb19; Immunoglobulin transcription factor 2; ITF-2; SL3-3 enhancer factor 2; SEF-2;
 
 

Transcript original information
Accession number AK122765.1
CAGE tag ID NA
EST ID NA
Clone Number PUAEN2003408
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (TCF4) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (TCF4);
Sequence data provider Project:FLJ; Provider:FLJ/HRI; 
Annotation project H-Invitational FLcDNA
Length of cDNA 2787[bp] (No. of exon:20)[A:700 T:615 G:730 C:742]
Devision HUM
Molecular type mRNA
Library origin Cell type pulmonary artery endothelial cells (HPAEC)
Tissue type NA
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) CAGCAG;  TAGCAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0022913
Genomic location  G-integra Help Chromosome 18
Location 18q21.2
Position 52895095- 53255860
Strand -
Possible duplicated location(s) NA
Gene structure 20 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:6925
KEGG GENES KEGG GENES(6925)
GeneCard GeneCardTCF4*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 HIP000062494
Predicted CDS 613..2616;  667[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.755

Motif information
ORF

length(667),orf(613:2616)
MHHQQRMAALGTDKELSDLLDFSAMFSPPVSSGKNGPTSLASGHFTGSNV
EDRSSSGSWGNGGHPSPSRNYGDGTPYDHMTSRDLGSHDNLSPPFVNSRI
QSKTERGSYSSYGRESNLQGCHQQSLLGGDMDMGNPGTLSPTKPGSQYYQ
YSSNNPRRRPLHSSAMEVQTKKVRKVPPGLPSSVYAPSASTADYNRDSPG
YPSSKPATSTFPSSFFMQDGHHSSDPWSSSGGMNQPGYAGMLGNSSHIPQ
SSSYCSLHPHERLSYPSHSSADINSSLPPMSTFHRSGTNHYSTSSCTPPA
NGTDSIMANRGSGAAGSSQTGDALGKALASIYSPDHTNNSFSSNPSTPVG
SPPSLSAGTAVWSRNGGQASSSPNYEGPLHSLQSRIEDRLERLDDAIHVL
RNHAVGPSTAMPGGHGDMHGIIGPSHNGAMGGLGSGYGTGLLSANRHSLM
VGTHREDGVALRGSHSLLPNQVPVPQLPVQSATSPDLNPPQDPYRGMPPG
LQGQSVSSGSSEIKSDDEGDENLQDTKSSEDKKLDDDKKDIKSITSNNDD
EDLTPEQKAEREKERRMANNARERLRVRDINEAFKELGRMVQLHLKSDKP
QTKLLILHQAVAVILSLEQQVRERNLNPKAACLKRREEEKVSSEPPPLSL
AGPHPGMGDASNHMGQM*
a.a.
length
InterPro Name
length(68), motif(556:623) 68 IPR011598 Myc-type, basic helix-loop-helix (bHLH) domain [Domain]
length(54), motif(564:617) 54 IPR011598 Myc-type, basic helix-loop-helix (bHLH) domain [Domain]
length(54), motif(565:618) 54 IPR011598 Myc-type, basic helix-loop-helix (bHLH) domain [Domain]
length(60), motif(565:624) 60 IPR011598 Myc-type, basic helix-loop-helix (bHLH) domain [Domain]
length(54), motif(570:623) 54 IPR011598 Myc-type, basic helix-loop-helix (bHLH) domain [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000042638
H-Inv cluster ID Locus viewHIX0022913
Accession number AK122765.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Transcription factor 4; TCF-4; Class B basic helix-loop-helix protein 19; bHLHb19; Immunoglobulin transcription factor 2; ITF-2; SL3-3 enhancer factor 2; SEF-2;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (P15884)  [Identity/coverage = 99.85%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 1681116210552823088609302263147020391548933416177791174362541743625517467953187280711923523821406692217892252204565122155184ALL
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 TCF4
HGNC aliases NA
HGNC name transcription factor 4
DDBJ NA
UniProt TCF4
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 HIP000062494
No. of interaction 7
Interaction partner(s) HIP000002890HIP000034631HIP000034631HIP000055065HIP000064410HIP000176869HIP000194532
BIND 150982; 
DIP 17E;  182238E; 
MINT MINT-4508065;  MINT-4508268;  MINT-4790867; 
HPRD 00011;  00241;  00242;  00243;  00286;  00536;  00590;  01071;  01166;  01302;  01414;  01435;  01753;  02437;  02608;  03428;  04000;  04078;  04694;  08935;  08980;  08995;  09581;  10423;  13634; 
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:6925
KEGG GENES KEGG GENES(6925)
GeneCard GeneCardTCF4*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 protein dimerization activity (GO:0046983); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT nuclear; 
Target P Other
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
560 637 1am9A 7e-13 26.7 75/80 a.38.1.1
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 AGhsA090517; 
Affymetrix
GeneChip
HG-Focus 203753_at; 
HG-U133 203753_at;  222146_s_at; 
HG-U133A 203753_at;  222146_s_at; 
HG-U133A_2 203753_at;  222146_s_at; 
HG-U133B NA
HG-U133_Plus_2 203753_at;  222146_s_at; 
HG-U95 56694_at;  68263_at;  68265_g_at;  89997_at; 
HG-U95A NA
HG-U95B 56694_at; 
HG-U95C NA
HG-U95D 68263_at;  68265_g_at;  89997_at; 
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 3789178;  3789180;  3808862;  3808865;  3808866;  3808870;  3808871;  3808890;  3808891;  3808892;  3808897;  3808899;  3808904;  3808905;  3808909;  3808922;  3808923;  3808938;  3808949;  3808950;  3808990;  3808993;  3808995;  3808996; 
HuGeneFL M74719_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P27332; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P27332; 
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:27-May-2015
Disease relation Disease name: Pitt-Hopkins syndrome (610954); 
Related information in OMIM OMIM ID:  602272;  Title: TRANSCRIPTION FACTOR 4
Co-localized orphan diseases NA
Disease related mutation MutationView:  602272
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(6925)
Disease Entrez Gene ID:(6925)
Substance Entrez Gene ID:(6925)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo ViewerLEGENDALEGENDA

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
39 .. 39 G/A rs141229144 - 5'UTR
160 .. 160 G/A rs113395332 - 5'UTR
592 .. 592 G/C rs113414846 - 5'UTR
696 .. 696 T/G rs199540114 - CDS Synonymous[Pro28Pro]
792 .. 792 G/A rs151203913 - CDS Synonymous[Gly60Gly]
821 .. 821 A/G rs200359873 - CDS Nonsynonymous[Asn70Ser]
842 .. 842 A/G rs76646268 - CDS Nonsynonymous[Tyr77Cys]
850 .. 850 A/G rs113943820 - CDS Nonsynonymous[Met80Val]
881 .. 881 A/G rs143244149 - CDS Nonsynonymous[Asn90Ser]
934 .. 934 T/C rs112222111 - CDS Nonsynonymous[Ser108Pro]
953 .. 953 G/A rs139876825 - CDS Nonsynonymous[Arg114Lys]
1024 .. 1024 A/G rs146412750 - CDS Nonsynonymous[Thr138Ala]
1026 .. 1026 C/G rs201061418 - CDS Synonymous[Thr138Thr]
1078 .. 1078 C/A rs200889338 - CDS Nonsynonymous[Pro156Thr]
1188 .. 1188 C/A rs143993583 - CDS Synonymous[Ala192Ala]
1196 .. 1196 A/G rs148573556 - CDS Nonsynonymous[Asn195Ser]
1216 .. 1216 C/T rs144835402 - CDS Nonsynonymous[Pro202Ser]
1272 .. 1272 C/T rs149861305 - CDS Synonymous[Gly220Gly]
1299 .. 1299 C/A rs200800656 - CDS Synonymous[Ser229Ser]
1318 .. 1318 C/G rs139859596 - CDS Nonsynonymous[Pro236Ala]
1379 .. 1379 G/C rs147305084 - CDS Nonsynonymous[Ser256Thr]
1409 .. 1409 C/T rs201776550 - CDS Nonsynonymous[Pro266Leu]
1419 .. 1419 C/T rs143896861 - CDS Synonymous[Ser269Ser]
1428 .. 1428 C/T rs138403996 - CDS Synonymous[Asp272Asp]
1556 .. 1556 C/T rs147445499 - CDS Nonsynonymous[Ala315Val]
1557 .. 1557 C/T rs200115299 - CDS Synonymous[Ala315Ala]
1578 .. 1578 T/C rs142998298 - CDS Synonymous[Asp322Asp]
1699 .. 1699 T/C rs113615316 - CDS Nonsynonymous[Ser363Pro]
1723 .. 1723 T/G rs75109886 - CDS Nonsynonymous[Ser371Ala]
1725 .. 1725 G/A rs148308964 - CDS Synonymous[Ser371Ser]
1765 .. 1765 C/T rs121909122 + CDS AA-STOP[Arg385*]
1769 .. 1769 T/C rs143594544 - CDS Nonsynonymous[Ile386Thr]
1806 .. 1806 T/C rs200225114 - CDS Synonymous[His398His]
1830 .. 1830 C/T rs201481787 - CDS Synonymous[Gly406Gly]
1857 .. 1857 T/C rs148909575 - CDS Synonymous[His415His]
1895 .. 1895 G/T rs186508321 - CDS Nonsynonymous[Gly428Val]
1898 .. 1898 C/T rs180788300 - CDS Nonsynonymous[Ala429Val]
1929 .. 1929 C/T rs200112082 - CDS Synonymous[Thr439Thr]
1962 .. 1962 G/A rs11660217 - CDS Nonsynonymous[Met450Ile]
1966 .. 1966 G/A rs138570124 - CDS Nonsynonymous[Gly452Arg]
2031 .. 2031 G/C rs143944746 - CDS Synonymous[Pro473Pro]
2150 .. 2150 T/C rs112174081 - CDS Nonsynonymous[Ile513Thr]
2163 .. 2163 C/T rs140862252 - CDS Synonymous[Asp517Asp]
2189 .. 2189 C/T rs202025804 - CDS Nonsynonymous[Thr526Met]
2251 .. 2251 A/G rs146454287 - CDS Nonsynonymous[Asn547Asp]
2283 .. 2283 G/A rs71368997 - CDS Synonymous[Gln557Gln]
2304 .. 2304 G/A rs144068462 - CDS Synonymous[Glu564Glu]
2333 .. 2333 G/C rs121909123 + CDS Nonsynonymous[Arg574Pro]
2338 .. 2338 C/T rs121909120 + CDS Nonsynonymous[Arg576Trp]
2339 .. 2339 G/A rs121909121 + CDS Nonsynonymous[Arg576Gln]
2466 .. 2466 G/A rs140078086 - CDS Synonymous[Glu618Glu]
2496 .. 2496 G/A rs200096408 - CDS Synonymous[Pro628Pro]
2505 .. 2505 G/A rs151150677 - CDS Synonymous[Ala631Ala]
2523 .. 2523 G/A rs76956936 - CDS Synonymous[Glu637Glu]
2541 .. 2541 A/G rs8766 + CDS Synonymous[Ser643Ser]
2552 .. 2552 C/G rs148802110 - CDS Nonsynonymous[Pro647Arg]
2565 .. 2565 C/T rs147289056 - CDS Synonymous[Ala651Ala]
2638 .. 2638 G/A rs182372608 - 3'UTR
2651 .. 2651 A/T rs190089558 - 3'UTR
2669 .. 2669 C/A rs111947783 - 3'UTR
2710 .. 2710 C/G rs141586028 - 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