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: HIT000048876 Accession number: AK129605 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Left-right determination factor 1; Left-right determination factor B; Protein lefty-1; Protein lefty-B; Precursor;
 
 

Transcript original information
Accession number AK129605.1
CAGE tag ID NA
EST ID NA
Clone Number RCT06932
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (LEFTY1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (LEFTY1);
Sequence data provider Project:FLJ; Provider:FLJ/IMSUT
Annotation project H-Invitational FLcDNA
Length of cDNA 1339[bp] (No. of exon:4)[A:264 T:279 G:403 C:393]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type rectum
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 1329(+) Signal: 1309-1313(+)
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 HIX0199988
Genomic location  G-integra Help Chromosome 1
Location 1q42.12
Position 226073982- 226076846
Strand -
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:10637
KEGG GENES KEGG GENES(10637)
GeneCard GeneCardLEFTY1*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 HIP000089514
Predicted CDS 81..884;  267[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.847

Motif information
ORF

length(267),orf(81:884)
MQPLWLCWALWVLPLASPGAALTGEQLLGSLLRQLQLKEVPTLDRADMEE
LVIPTHVRAQYVALLQRSHGDRSRGKRFSQSFREVAGRFLALEASTHLLL
QVSVQREHLGPLASGAHKLVRFASQGAPAGLGEPQLELHTLDLGDYGAQG
DCDPEAPMTEGTRCCRQEMYIDLQGMKWAENWVLEPPGFLAYECVGTCRQ
PPEALAFKWPFLGPRQCIASETDSLPMIVSIKEGGRTRPQVVSLPNMRVQ
KCSCASDGALVPRRLQP*
a.a.
length
InterPro Name
length(255), motif(1:255) 255 IPR015615 Transforming growth factor-beta-related [Family]
length(23), motif(4:26) 23 IPR003942 Left- Right determination factor [Family]
length(22), motif(26:47) 22 IPR003942 Left- Right determination factor [Family]
length(17), motif(49:65) 17 IPR003942 Left- Right determination factor [Family]
length(19), motif(72:90) 19 IPR003942 Left- Right determination factor [Family]
length(113), motif(143:255) 113 IPR001839 Transforming growth factor-beta, C-terminal [Domain]
length(96), motif(159:254) 96 IPR029034 Cystine-knot cytokine [Domain]
length(95), motif(160:254) 95 IPR029034 Cystine-knot cytokine [Domain]
length(40), motif(163:202) 40 IPR001839 Transforming growth factor-beta, C-terminal [Domain]
length(92), motif(164:255) 92 IPR001839 Transforming growth factor-beta, C-terminal [Domain]
length(16), motif(183:198) 16 IPR017948 Transforming growth factor beta, conserved site [Conserved_site]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000048876
H-Inv cluster ID Locus viewHIX0199988
Accession number AK129605.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Similar to Left-right determination factor 1; Left-right determination factor B; Protein lefty-1; Protein lefty-B; Precursor;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (O75610)  [Identity/coverage = 99.561%/89.34%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 10053005129753091548933416710414ALL
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 LEFTY1
HGNC aliases "left-right determination, factor B"
HGNC name left-right determination factor 1
DDBJ NA
UniProt LEFTY1
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 HIP000089514
No. of interaction 1
Interaction partner(s) HIP000146718
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:10637
KEGG GENES KEGG GENES(10637)
GeneCard GeneCardLEFTY1*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 growth factor activity (GO:0008083);  transforming growth factor beta receptor binding (GO:0005160); 
Biological process cell growth (GO:0016049); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT extracellular;  lysosome;  mitochondria;  nuclear; 
Target P signal peptide
SOSUI membrane 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
163 254 1bmpA 1e-16 25.0 88/104 g.17.1.2
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL endocrine_exocrine; 
Probe
information DNAProbeLocator
AceGene NA
Affymetrix
GeneChip
HG-Focus 206268_at; 
HG-U133 206268_at; 
HG-U133A 206268_at; 
HG-U133A_2 206268_at; 
HG-U133B NA
HG-U133_Plus_2 206268_at; 
HG-U95 35932_at; 
HG-U95A 35932_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2458581;  2458583;  2458590;  2458591; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P160336; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P160336; 
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
23 .. 23 C/A rs139832223 - 5'UTR
29 ^ 30 -/A rs35720599 - 5'UTR
71 .. 71 G/A rs35310234 - 5'UTR
178 .. 178 G/A rs41310561 - CDS Nonsynonymous[Arg33Gln]
248 .. 248 C/T rs140535323 - CDS Synonymous[His56His]
249 .. 249 G/A rs35273824 - CDS Nonsynonymous[Val57Met]
264 .. 264 G/A rs61995951 - CDS Nonsynonymous[Val62Met]
288 .. 288 G/A rs149725453 - CDS Nonsynonymous[Gly70Arg]
294 .. 294 C/T rs202024911 - CDS Nonsynonymous[Arg72Cys]
296 .. 296 C/T rs139545692 - CDS Synonymous[Arg72Arg]
302 .. 302 C/A rs138826949 - CDS Synonymous[Arg74Arg]
303 .. 303 G/A rs146054726 - CDS Nonsynonymous[Gly75Arg]
318 .. 318 C/T rs148172390 - CDS AA-STOP[Gln80*]
355 .. 355 T/C rs145431393 - CDS Nonsynonymous[Leu92Ser]
450 .. 450 T/C rs201517157 - CDS Nonsynonymous[Ser124Pro]
461 .. 461 G/T rs145906534 - CDS Synonymous[Ala127Ala]
471 .. 471 C/T rs201650960 - CDS Nonsynonymous[Leu131Phe]
476 .. 476 G/A rs41303105 - CDS Synonymous[Gly132Gly]
492 .. 492 C/G rs200296829 - CDS Nonsynonymous[Leu138Val]
549 .. 549 C/T rs147571576 - CDS Nonsynonymous[Pro157Ser]
558 .. 558 G/A rs139440539 - CDS Nonsynonymous[Glu160Lys]
558 .. 558 G/A rs75429575 - CDS Nonsynonymous[Glu160Lys]
584 .. 584 G/C rs148675652 - CDS Nonsynonymous[Glu168Asp]
607 .. 607 T/C rs201362049 - CDS Nonsynonymous[Met176Thr]
618 .. 618 G/A rs146485828 - CDS Nonsynonymous[Glu180Lys]
640 .. 640 C/T rs146082781 - CDS Nonsynonymous[Pro187Leu]
676 .. 676 G/A rs61739581 - CDS Nonsynonymous[Arg199Gln]
685 .. 685 C/T rs150915411 - CDS Nonsynonymous[Pro202Leu]
697 .. 697 C/A rs202201616 - CDS Nonsynonymous[Ala206Asp]
703 .. 703 A/C rs201076564 - CDS Nonsynonymous[Lys208Thr]
710 .. 710 G/A rs146733248 - CDS Synonymous[Pro210Pro]
717 .. 717 G/A rs143958321 - CDS Nonsynonymous[Gly213Arg]
722 .. 722 T/G rs143474754 - CDS Synonymous[Pro214Pro]
723 .. 723 C/G rs200607882 - CDS Nonsynonymous[Arg215Gly]
739 .. 739 C/G rs117876231 - CDS Nonsynonymous[Ser220Trp]
748 .. 748 A/C rs360057 - CDS Nonsynonymous[Asp223Ala]
854 .. 854 T/G rs146506148 - CDS Synonymous[Gly258Gly]
871 .. 871 G/A rs139254695 - CDS Nonsynonymous[Arg264Lys]
875 .. 875 C/G rs35684337 - CDS Synonymous[Leu265Leu]
882 .. 882 T/C rs141038694 - CDS STOP-AA[*268Gln]
889 .. 889 C/A rs56769658 - 3'UTR
906 .. 906 G/A rs200925389 - 3'UTR
938 .. 938 G/T rs3766941 - 3'UTR
963 .. 963 A/G rs41315436 - 3'UTR
974 .. 974 G/A rs76469045 - 3'UTR
988 .. 988 C/T rs189294996 - 3'UTR
990 .. 990 G/A rs41315438 - 3'UTR
1022 .. 1022 C/T rs142585586 - 3'UTR
1039 .. 1039 C/T rs148425461 - 3'UTR
1070 .. 1070 T/C rs185315202 - 3'UTR
1148 .. 1148 G/A rs180867518 - 3'UTR
1200 .. 1200 G/C rs41307698 - 3'UTR
1221 .. 1221 T/C rs200851219 + 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