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: HIT000252917 Accession number: AY358873 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Left-right determination factor 1; Left-right determination factor B; Protein lefty-1; Protein lefty-B; Precursor;
 
 

Transcript original information
Accession number AY358873.1
CAGE tag ID NA
EST ID NA
Clone Number DNA33461
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 NA
Annotation project NA
Length of cDNA 1616[bp] (No. of exon:4)[A:294 T:318 G:506 C:497]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
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) 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 226073979- 226076833
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 HIP000089515
Predicted CDS 68..1168;  366[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.86
Database links RefSeq NP_066277
UniProt O75610
CCDS CCDS1548

Motif information
ORF

length(366),orf(68:1168)
MQPLWLCWALWVLPLASPGAALTGEQLLGSLLRQLQLKEVPTLDRADMEE
LVIPTHVRAQYVALLQRSHGDRSRGKRFSQSFREVAGRFLALEASTHLLV
FGMEQRLPPNSELVQAVLRLFQEPVPKAALHRHGRLSPRSARARVTVEWL
RVRDDGSNRTSLIDSRLVSVHESGWKAFDVTEAVNFWQQLSRPRQPLLLQ
VSVQREHLGPLASGAHKLVRFASQGAPAGLGEPQLELHTLDLGDYGAQGD
CDPEAPMTEGTRCCRQEMYIDLQGMKWAENWVLEPPGFLAYECVGTCRQP
PEALAFKWPFLGPRQCIASETDSLPMIVSIKEGGRTRPQVVSLPNMRVQK
CSCASDGALVPRRLQP*
a.a.
length
InterPro Name
length(354), motif(1:354) 354 IPR015615 Transforming growth factor-beta-related [Family]
length(23), motif(4:26) 23 IPR003942 Left- Right determination factor [Family]
length(190), motif(22:211) 190 IPR001111 Transforming growth factor-beta, N-terminal [Domain]
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(16), motif(97:112) 16 IPR003942 Left- Right determination factor [Family]
length(21), motif(112:132) 21 IPR003942 Left- Right determination factor [Family]
length(19), motif(132:150) 19 IPR003942 Left- Right determination factor [Family]
length(22), motif(153:174) 22 IPR003942 Left- Right determination factor [Family]
length(24), motif(187:210) 24 IPR003942 Left- Right determination factor [Family]
length(16), motif(216:231) 16 IPR003942 Left- Right determination factor [Family]
length(26), motif(234:259) 26 IPR003942 Left- Right determination factor [Family]
length(113), motif(242:354) 113 IPR001839 Transforming growth factor-beta, C-terminal [Domain]
length(95), motif(259:353) 95 IPR029034 Cystine-knot cytokine [Domain]
length(40), motif(262:301) 40 IPR001839 Transforming growth factor-beta, C-terminal [Domain]
length(92), motif(263:354) 92 IPR001839 Transforming growth factor-beta, C-terminal [Domain]
length(22), motif(265:286) 22 IPR003942 Left- Right determination factor [Family]
length(16), motif(282:297) 16 IPR017948 Transforming growth factor beta, conserved site [Conserved_site]
length(21), motif(299:319) 21 IPR003942 Left- Right determination factor [Family]
length(20), motif(325:344) 20 IPR003942 Left- Right determination factor [Family]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000252917
H-Inv cluster ID Locus viewHIX0199988
Accession number AY358873.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Left-right determination factor 1; Left-right determination factor B; Protein lefty-1; Protein lefty-B; Precursor;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (O75610)  [Identity/coverage = 100.0%/100.0%] 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 HIP000089515
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: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 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 growth factor activity (GO:0008083);  transforming growth factor beta receptor binding (GO:0005160); 
Biological process cell growth (GO:0016049);  growth (GO:0040007); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT extracellular;  lysosome;  mitochondria;  Other; 
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
262 353 1bmpA 8e-17 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

Evolutionary information  Evola Help Last modified:27-May-2015
Relationship Species Accession number MGI Links
Orthology Gallus sp. (Chicken) AB031398 G-integraG-integra
Orthology Mus sp. (Mouse) AK131943 MGI:3532224 G-integraG-integra
Orthology Oryzias sp. (Medaka) EF206722 G-integraG-integra
Orthology Macaca sp. (Macaque) ENSMMUT00000008117 G-integraG-integra
Orthology Pongo sp. (Orangutan) ENSPPYT00000000185 G-integraG-integra
Orthology Tetraodon sp. (Tetraodon) GSTENT00018477001 G-integraG-integra
Orthology Takifugu sp. (Fugu) SINFRUT00000154042 G-integraG-integra
Orthology Rattus sp. (Rat) XM_001061810 G-integraG-integra
Orthology Pan sp. (Chimpanzee) XM_001138156 G-integraG-integra
Orthology Monodelphis sp. (Opossum) XM_001376637 G-integraG-integra
Orthology Bos sp. (Cow) XM_613627 G-integraG-integra
Orthology Canis sp. (Dog) XM_849632 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
10 .. 10 C/A rs139832223 - 5'UTR
16 ^ 17 -/A rs35720599 - 5'UTR
58 .. 58 G/A rs35310234 - 5'UTR
165 .. 165 G/A rs41310561 - CDS Nonsynonymous[Arg33Gln]
235 .. 235 C/T rs140535323 - CDS Synonymous[His56His]
236 .. 236 G/A rs35273824 - CDS Nonsynonymous[Val57Met]
251 .. 251 G/A rs61995951 - CDS Nonsynonymous[Val62Met]
275 .. 275 G/A rs149725453 - CDS Nonsynonymous[Gly70Arg]
281 .. 281 C/T rs202024911 - CDS Nonsynonymous[Arg72Cys]
283 .. 283 C/T rs139545692 - CDS Synonymous[Arg72Arg]
289 .. 289 C/A rs138826949 - CDS Synonymous[Arg74Arg]
290 .. 290 G/A rs146054726 - CDS Nonsynonymous[Gly75Arg]
305 .. 305 C/T rs148172390 - CDS AA-STOP[Gln80*]
342 .. 342 T/C rs145431393 - CDS Nonsynonymous[Leu92Ser]
442 .. 442 C/T rs12753531 - CDS Synonymous[Val125Val]
492 .. 492 G/A rs191758097 - CDS Nonsynonymous[Arg142Gln]
587 .. 587 G/C rs201293717 - CDS Nonsynonymous[Gly174Arg]
593 .. 593 A/G rs200306047 - CDS Nonsynonymous[Lys176Glu]
734 .. 734 T/C rs201517157 - CDS Nonsynonymous[Ser223Pro]
745 .. 745 G/T rs145906534 - CDS Synonymous[Ala226Ala]
755 .. 755 C/T rs201650960 - CDS Nonsynonymous[Leu230Phe]
760 .. 760 G/A rs41303105 - CDS Synonymous[Gly231Gly]
776 .. 776 C/G rs200296829 - CDS Nonsynonymous[Leu237Val]
833 .. 833 C/T rs147571576 - CDS Nonsynonymous[Pro256Ser]
842 .. 842 G/A rs139440539 - CDS Nonsynonymous[Glu259Lys]
842 .. 842 G/A rs75429575 - CDS Nonsynonymous[Glu259Lys]
868 .. 868 G/C rs148675652 - CDS Nonsynonymous[Glu267Asp]
891 .. 891 T/C rs201362049 - CDS Nonsynonymous[Met275Thr]
902 .. 902 G/A rs146485828 - CDS Nonsynonymous[Glu279Lys]
924 .. 924 C/T rs146082781 - CDS Nonsynonymous[Pro286Leu]
960 .. 960 G/A rs61739581 - CDS Nonsynonymous[Arg298Gln]
969 .. 969 C/T rs150915411 - CDS Nonsynonymous[Pro301Leu]
981 .. 981 C/A rs202201616 - CDS Nonsynonymous[Ala305Asp]
987 .. 987 A/C rs201076564 - CDS Nonsynonymous[Lys307Thr]
994 .. 994 G/A rs146733248 - CDS Synonymous[Pro309Pro]
1001 .. 1001 G/A rs143958321 - CDS Nonsynonymous[Gly312Arg]
1006 .. 1006 T/G rs143474754 - CDS Synonymous[Pro313Pro]
1007 .. 1007 C/G rs200607882 - CDS Nonsynonymous[Arg314Gly]
1023 .. 1023 C/G rs117876231 - CDS Nonsynonymous[Ser319Trp]
1032 .. 1032 A/C rs360057 - CDS Nonsynonymous[Asp322Ala]
1138 .. 1138 T/G rs146506148 - CDS Synonymous[Gly357Gly]
1155 .. 1155 G/A rs139254695 - CDS Nonsynonymous[Arg363Lys]
1159 .. 1159 C/G rs35684337 - CDS Synonymous[Leu364Leu]
1166 .. 1166 T/C rs141038694 - CDS STOP-AA[*367Gln]
1173 .. 1173 C/A rs56769658 - 3'UTR
1190 .. 1190 G/A rs200925389 - 3'UTR
1222 .. 1222 G/T rs3766941 - 3'UTR
1247 .. 1247 A/G rs41315436 - 3'UTR
1258 .. 1258 G/A rs76469045 - 3'UTR
1272 .. 1272 C/T rs189294996 - 3'UTR
1274 .. 1274 G/A rs41315438 - 3'UTR
1306 .. 1306 C/T rs142585586 - 3'UTR
1323 .. 1323 C/T rs148425461 - 3'UTR
1354 .. 1354 T/C rs185315202 - 3'UTR
1432 .. 1432 G/A rs180867518 - 3'UTR
1484 .. 1484 G/C rs41307698 - 3'UTR
1505 .. 1505 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