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: HIT000090726 Accession number: BC022998 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Structural maintenance of chromosomes protein 6.
 
 

Transcript original information
Accession number BC022998.1
CAGE tag ID NA
EST ID NA
Clone Number IMAGE:4386550
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (SMC6) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (SMC6);
Sequence data provider NA
Annotation project NA
Length of cDNA 1087[bp] (No. of exon:8)[A:411 T:277 G:216 C:183]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Bone, osteosarcoma
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature N/C-truncated
Kozak sequence NA
PolyA Site: 1073(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) TAGGAG; 
Transcript quality feature Truncation; 
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0001845
Genomic location  G-integra Help Chromosome 2
Location 2p24.2
Position 17877601- 17897463
Strand -
Possible duplicated location(s) NA
Gene structure 8 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:79677
KEGG GENES KEGG GENES(79677)
GeneCard GeneCardSMC6*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 HIP000017673
Predicted CDS 3..1087;  361[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.662

Motif information
ORF

length(361),orf(3:1087)
KTDRLKRFGPNVPALLEAIDDAYRQGHFTYKPVGPLGACIHLRDPELALA
IESCLKGLLQAYCCHNHADERVLQALMKRFYLPGTSRPPIIVSEFRNEIY
DVRHRAAYHPDFPTVLTALEIDNAVVANSLIDMRGIETVLLIKNNSVARA
VMQSQKPPKNCREAFTADGDQVFAGRYYSSENTRPKFLSRDVDSEISDLE
NEVENKTAQILNLQQHLSALEKDIKHNEELLKRCQLHYKELKMKIRKNIS
EIRELENIEEHQSVDIATLEDEAQENKSKMKMVEEHMEQQKENMEHLKSL
KIEAENKYDAIKFKINQLSELADPLKDELNLADSEVDNQKRGKRHYEEKQ
KEHLDTLKKKK
a.a.
length
InterPro Name
length(361), motif(1:361) 361 IPR027132 Structural maintenance of chromosomes protein 6 [Family]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000090726
H-Inv cluster ID Locus viewHIX0001845
Accession number BC022998.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Similar to Structural maintenance of chromosomes protein 6.
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (NP_001135758)  [Identity/coverage = 99.446%/33.09%] 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 SMC6
HGNC aliases "SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"
HGNC name structural maintenance of chromosomes 6
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 HIP000017673
No. of interaction 1
Interaction partner(s) HIP000357239
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:79677
KEGG GENES KEGG GENES(79677)
GeneCard GeneCardSMC6*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 DNA repair (GO:0006281);  double-strand break repair via homologous recombination (GO:0000724); 
Cellular component Smc5-Smc6 complex (GO:0030915); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT cytosol;  nuclear;  peroxisome; 
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.

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsA061114; 
Affymetrix
GeneChip
HG-Focus NA
HG-U133 NA
HG-U133A NA
HG-U133A_2 NA
HG-U133B NA
HG-U133_Plus_2 NA
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2541962;  2541963;  2541964;  2541965;  2541966;  2541967;  2541968;  2541969;  2541971;  2541972; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 NA
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
30 .. 30 C/G rs185599983 - CDS Nonsynonymous[Pro10Ala]
49 .. 49 T/C rs113186456 - CDS Nonsynonymous[Leu16Pro]
71 .. 71 T/C rs138554068 - CDS Synonymous[Tyr23Tyr]
130 .. 130 G/A rs202190810 - CDS Nonsynonymous[Arg43Gln]
173 .. 173 G/A rs183880008 - CDS Synonymous[Gly57Gly]
188 .. 188 T/C rs145245598 - CDS Synonymous[Tyr62Tyr]
215 .. 215 G/T rs143591666 - CDS Nonsynonymous[Arg71Ser]
236 .. 236 A/G rs145642076 - CDS Synonymous[Lys78Lys]
288 .. 288 C/T rs201267935 - CDS Nonsynonymous[Arg96Trp]
297 .. 297 A/G rs192935709 - CDS Nonsynonymous[Ile99Val]
318 .. 318 G/A rs142172161 - CDS Nonsynonymous[Ala106Thr]
374 .. 374 G/A rs144764638 - CDS Synonymous[Ala124Ala]
419 .. 419 G/A rs6711251 - CDS Synonymous[Val139Val]
640 .. 640 T/C rs199960484 - CDS Nonsynonymous[Leu213Pro]
657 .. 657 G/A rs1065381 + CDS Nonsynonymous[Ala219Thr]
760 .. 760 G/A rs189584906 - CDS Nonsynonymous[Arg253Gln]
862 .. 862 T/C rs111884371 - CDS Nonsynonymous[Met287Thr]
 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