H-InvDB x AHG DB
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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000084895 Accession number: AY166859 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Protein lin-9 homolog isoform 1.
 
 

Transcript original information
Accession number AY166859.1
CAGE tag ID NA
EST ID NA
Clone Number NA
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (LIN9) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (LIN9);
Sequence data provider NA
Annotation project NA
Length of cDNA 2138[bp] (No. of exon:13)[A:575 T:454 G:555 C:554]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type testis
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) CAGAAG; 
Transcript quality feature NMD predicted;  Truncation; 
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0023586
Genomic location  G-integra Help Chromosome 1
Location 1q42.12
Position 226421111- 226497434
Strand -
Possible duplicated location(s) NA
Gene structure 13 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:286826
KEGG GENES KEGG GENES(286826)
GeneCard GeneCardLIN9*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 HIP000093667
Predicted CDS 145..1785;  546[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.686

Motif information
ORF

length(546),orf(145:1785)
MRPRTEGFFPPAGASLPFSTRNKQPAVPAAAARAAEHAPGAGPGRDSGAG
TAPPALRRRASPCGLLPPFLPPGSAGGGGGGARRGPPSAAPPPRAGAGGA
GPASASRGGSSAARRRGQRAPHSNLPRKDSLRPTMHRGGQPLKKRRGSSK
MAELDQLPDESSSAKALVSLKEGSLSNTWNEKYSSLQKTPVWKGRNTSSA
VEMPFRNSKRSRLFSDEDDRQINTRSPKRNQRVAMVPQKFTATMSTPDKK
ASQKIGFRLRNLLKLPKAHKWCIYEWFYSNIDKPLFEGDNDFCVCLKESF
PNLKTRKLTRVEWGKIRRLMGKPRRCSSAFFEEERSALKQKRQKIRLLQQ
RKVADVSQFKDLPDEIPLPLVIGTKVTARLRGVHDGLFTGQIDAVDTLNA
TYRVTFDRTGLGTHTIPDYEVLSNEPHETMPIAALGQKQRPSRFFMTPPR
LHYTPPLQSPIIDNDPLLGQSPWRSKISGSDTETLGGFPVEFLIQVTRLS
KILMIHQGTYQEHQGHEHRSRNTGNHIACQSALDSRGDLRQSVSGT*
a.a.
length
InterPro Name
length(404), motif(102:505) 404 IPR010561 Protein LIN-9/Protein ALWAYS EARLY [Family]
length(105), motif(277:381) 105 IPR010561 Protein LIN-9/Protein ALWAYS EARLY [Family]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000084895
H-Inv cluster ID Locus viewHIX0023586
Accession number AY166859.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Similar to Protein lin-9 homolog isoform 1.
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (NP_775106)  [Identity/coverage = 89.149%/84.59%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
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 LIN9
HGNC aliases "lin-9 homolog (C. elegans)"
HGNC name lin-9 DREAM MuvB core complex component
DDBJ NA
UniProt NA
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 HIP000093667
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:286826
KEGG GENES KEGG GENES(286826)
GeneCard GeneCardLIN9*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
Biological process cell cycle (GO:0007049);  transcription, DNA-dependent (GO:0006351); 
Cellular component transcriptional repressor complex (GO:0017053); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT nuclear;  cytosol;  mitochondria;  Other; 
Target P Not predicted
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.

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsC260921; 
Affymetrix
GeneChip
HG-Focus NA
HG-U133 NA
HG-U133A NA
HG-U133A_2 NA
HG-U133B NA
HG-U133_Plus_2 1552771_a_at; 
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2383145;  2458753;  2458754;  2458755;  2458756;  2458757;  2458758;  2458759;  2458760;  2458762;  2458763;  2458764;  2458769;  2458770;  2458771;  2458772; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P301995; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P301995; 
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
16 .. 16 C/T rs79928746 - 5'UTR
46 .. 46 G/T rs2666424 + 5'UTR
53 .. 53 G/A rs187594887 - 5'UTR
137 .. 137 C/- rs35658897 - 5'UTR
179 .. 179 C/T rs150096442 - CDS Nonsynonymous[Ala12Val]
207 .. 207 G/C rs182039657 - CDS Synonymous[Arg21Arg]
504 .. 504 T/G rs200214743 - CDS Synonymous[Ala120Ala]
587 .. 587 C/T/G rs147594769 - CDS
588 .. 588 G/A rs141137602 - CDS Synonymous[Ser148Ser]
613 .. 613 T/G rs142246298 - CDS Nonsynonymous[Leu157Val]
615 .. 615 G/T rs200253990 - CDS Nonsynonymous[Leu157Phe]
654 .. 654 A/G rs188672834 - CDS Synonymous[Leu170Leu]
678 .. 678 G/A rs201383597 - CDS Synonymous[Thr178Thr]
715 .. 715 G/A rs144076944 - CDS Nonsynonymous[Val191Ile]
724 .. 724 G/T rs75027947 - CDS Nonsynonymous[Gly194Cys]
730 .. 730 A/C rs147158007 - CDS Nonsynonymous[Asn196His]
799 .. 799 G/C rs201015210 - CDS Nonsynonymous[Asp219His]
803 ^ 804 -/G rs34204557 - CDS
847 .. 847 A/G rs201055360 - CDS Nonsynonymous[Met235Val]
936 .. 936 G/A rs201968099 - CDS Synonymous[Lys264Lys]
966 .. 966 C/T rs142841984 - CDS Synonymous[Tyr274Tyr]
1020 .. 1020 T/C rs10799347 - CDS Synonymous[Phe292Phe]
1065 .. 1065 G/A rs143380168 - CDS Synonymous[Lys307Lys]
1080 .. 1080 A/G rs142541127 - CDS Synonymous[Glu312Glu]
1223 .. 1223 A/C rs200594612 - CDS Nonsynonymous[Lys360Thr]
1296 .. 1296 T/C rs192543474 - CDS Synonymous[His384His]
1318 .. 1318 A/T rs200701978 - CDS Nonsynonymous[Ile392Leu]
1335 .. 1335 T/A rs146968727 - CDS Synonymous[Thr397Thr]
1390 .. 1390 A/G rs199567702 - CDS Nonsynonymous[Ile416Val]
1493 .. 1493 G/A rs201671299 - CDS Nonsynonymous[Arg450Gln]
1510 .. 1510 C/T rs149663129 - CDS Nonsynonymous[Pro456Ser]
1533 .. 1533 T/C rs113700764 - CDS Synonymous[Asp463Asp]
1536 .. 1536 T/C rs112266260 - CDS Synonymous[Asn464Asn]
1542 .. 1542 T/C rs151010513 - CDS Synonymous[Pro466Pro]
1557 .. 1557 G/A rs144126698 - CDS Synonymous[Ser471Ser]
1573 .. 1573 A/C rs144324813 - CDS Nonsynonymous[Ile477Leu]
1757 .. 1757 A/G rs139603309 - CDS Nonsynonymous[Asp538Gly]
1764 .. 1764 A/G rs149356682 - CDS Synonymous[Arg540Arg]
1871 .. 1871 A/G rs144086241 - 3'UTR
1906 .. 1906 A/C rs138510303 - 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