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: HIT000242845 Accession number: AF190323 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Protein lin-9 homolog isoform 2.
 
 

Transcript original information
Accession number AF190323.1
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 2909[bp] (No. of exon:14)[A:995 T:904 G:534 C:476]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type NA
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature N-truncated
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGAAG; 
Transcript quality feature NA
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 226418850- 226496873
Strand -
Possible duplicated location(s) NA
Gene structure 14 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 HIP000346418
Predicted CDS 1..1557;  518[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.693

Motif information
ORF

length(518),orf(1:1557)
QPLKKRRGSFKMAELDQLPDESSSAKALVSLKEGSLSNTWNEKYSSLQKT
PVWKGRNTSSAVEMKFTATMSTPDKKASQKIGFRLRNLLKLPKAHKWCIY
EWFYSNIDKPLFEGDNDFCVCLKESFPNLKTRKLTRVEWGKIRRLMGKPR
RCSSAFFEEERSALKQKRQKIRLLQQRKVADVSQFKDLPDEIPLPLVIGT
KVTARLRGVHDGLFTGQIDAVDTLNATYRVTFDRTGLGTHTIPDYEVLSN
EPHETMPIAAFGQKQRPSRFFMTPPRLHYTPPLQSPIIDNDPLLGQSPWR
SKISGSDTETLGGFPVEFLIQVTRLSKILMIKKEHIKKLREMNTEAEKLK
SYSMPISIEFQRRYATIVLELEQLNKDLNKVLHKVQQYCYELAPDQGLQP
ADQPTDMRRRCEEEAQEIVRHANSSTGQPCVENENLTDLISRLTAILLQI
KCLAEGGDLNSFEFKSLTDSLNDIKSTIDASNISCFQNNVEIHVAHIQSG
LSQMGNLHAFAANNTNRD*
a.a.
length
InterPro Name
length(514), motif(5:518) 514 IPR010561 Protein LIN-9/Protein ALWAYS EARLY [Family]
length(105), motif(103:207) 105 IPR010561 Protein LIN-9/Protein ALWAYS EARLY [Family]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000242845
H-Inv cluster ID Locus viewHIX0023586
Accession number AF190323.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Similar to Protein lin-9 homolog isoform 2.
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (NP_001257338)  [Identity/coverage = 100.0%/99.04%] 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 BARA
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 HIP000346418
No. of interaction 4
Interaction partner(s) HIP000065282HIP000085973HIP000217068HIP000243385
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;  extracellular; 
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 NA
Affymetrix
GeneChip
HG-Focus NA
HG-U133 230365_at;  235039_x_at; 
HG-U133A NA
HG-U133A_2 NA
HG-U133B 230365_at;  235039_x_at; 
HG-U133_Plus_2 1552771_a_at;  230365_at;  235039_x_at; 
HG-U95 62603_r_at;  81497_at; 
HG-U95A NA
HG-U95B NA
HG-U95C 62603_r_at; 
HG-U95D NA
HG-U95E 81497_at; 
HG-U95Av2 NA
HuEx-1_0 2383131;  2458743;  2458744;  2458745;  2458747;  2458748;  2458749;  2458753;  2458754;  2458755;  2458756;  2458757;  2458758;  2458759;  2458760;  2458763;  2458764;  2458769; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P301995; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P301995;  A_32_P233304; 
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
26 .. 26 C/T/G rs147594769 - CDS
27 .. 27 G/A rs141137602 - CDS Synonymous[Ser9Ser]
52 .. 52 T/G rs142246298 - CDS Nonsynonymous[Leu18Val]
54 .. 54 G/T rs200253990 - CDS Nonsynonymous[Leu18Phe]
93 .. 93 A/G rs188672834 - CDS Synonymous[Leu31Leu]
117 .. 117 G/A rs201383597 - CDS Synonymous[Thr39Thr]
154 .. 154 G/A rs144076944 - CDS Nonsynonymous[Val52Ile]
163 .. 163 G/T rs75027947 - CDS Nonsynonymous[Gly55Cys]
169 .. 169 A/C rs147158007 - CDS Nonsynonymous[Asn57His]
270 .. 270 G/A rs201968099 - CDS Synonymous[Lys90Lys]
300 .. 300 C/T rs142841984 - CDS Synonymous[Tyr100Tyr]
354 .. 354 T/C rs10799347 - CDS Synonymous[Phe118Phe]
399 .. 399 G/A rs143380168 - CDS Synonymous[Lys133Lys]
414 .. 414 A/G rs142541127 - CDS Synonymous[Glu138Glu]
557 .. 557 A/C rs200594612 - CDS Nonsynonymous[Lys186Thr]
630 .. 630 T/C rs192543474 - CDS Synonymous[His210His]
652 .. 652 A/T rs200701978 - CDS Nonsynonymous[Ile218Leu]
669 .. 669 T/A rs146968727 - CDS Synonymous[Thr223Thr]
724 .. 724 A/G rs199567702 - CDS Nonsynonymous[Ile242Val]
827 .. 827 G/A rs201671299 - CDS Nonsynonymous[Arg276Gln]
844 .. 844 C/T rs149663129 - CDS Nonsynonymous[Pro282Ser]
867 .. 867 T/C rs113700764 - CDS Synonymous[Asp289Asp]
870 .. 870 T/C rs112266260 - CDS Synonymous[Asn290Asn]
876 .. 876 T/C rs151010513 - CDS Synonymous[Pro292Pro]
891 .. 891 G/A rs144126698 - CDS Synonymous[Ser297Ser]
907 .. 907 A/C rs144324813 - CDS Nonsynonymous[Ile303Leu]
1089 .. 1089 A/G rs139603309 - CDS Synonymous[Arg363Arg]
1096 .. 1096 A/G rs149356682 - CDS Nonsynonymous[Thr366Ala]
1203 .. 1203 A/G rs144086241 - CDS Synonymous[Ala401Ala]
1211 .. 1211 C/A rs200459254 - CDS Nonsynonymous[Pro404Gln]
1241 .. 1241 A/C rs138510303 - CDS Nonsynonymous[Glu414Ala]
1290 .. 1290 C/T rs142771300 - CDS Synonymous[Cys430Cys]
1374 .. 1374 C/T rs149035186 - CDS Synonymous[Asp458Asp]
1407 .. 1407 C/G rs145608178 - CDS Nonsynonymous[Asp469Glu]
1419 .. 1419 T/C rs140382721 - CDS Synonymous[Asp473Asp]
1522 .. 1522 C/T rs182468793 - CDS Nonsynonymous[His508Tyr]
1623 .. 1623 G/A rs141392755 - 3'UTR
1719 .. 1719 A/G rs61836886 - 3'UTR
1952 .. 1952 G/A rs190646593 - 3'UTR
2187 .. 2187 T/A rs111497688 - 3'UTR
2326 .. 2326 A/T rs187348202 - 3'UTR
2349 .. 2349 T/C rs184060115 - 3'UTR
2363 .. 2363 T/- rs112592704 - 3'UTR
2522 .. 2522 G/C rs2377028 + 3'UTR
2593 .. 2593 C/G rs2377029 + 3'UTR
2623 .. 2623 G/A rs148302888 - 3'UTR
2638 .. 2638 G/A rs143275101 - 3'UTR
2824 .. 2824 T/A rs149174065 - 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