H-InvDB_9.0 released on May 27, 2015.
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H-Inv ID (HIT)
H-Inv cluster ID (HIX)
H-Inv protein ID (HIP)
H-Inv gene family/group (HIF)
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Chromosome number
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Definition*
Data source ID
---
CCDS ID
dbSNP ID (rs number)
EC number
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FR ID
FR Accession number
GO ID
GO name*
HGNC gene symbol
HGNC gene name*
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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.
Select format
Flat file
XML file
Nucleotide sequence fasta
Protein sequence fasta
Transcript original information
Accession number
BC022998.1
CAGE tag ID
NA
EST ID
NA
Clone Number
IMAGE:4386550
Experimental resources
NBRC
;
HGPD
;
Antibody (SMC6)
;
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
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
GTAAAACTGATCGACTCAAAAGATTTGGCCCTAATGTTCCAGCTCTTCTT GAAGCCATAGATGATGCTTATAGACAAGGACATTTTACCTATAAACCTGT AGGCCCTTTAGGAGCTTGCATTCATCTTCGGGACCCAGAACTTGCTTTGG CTATTGAATCTTGCTTAAAAGGGCTTCTGCAGGCCTATTGTTGCCATAAT CATGCTGATGAAAGGGTCCTTCAGGCACTCATGAAAAGGTTTTATTTACC AGGGACCTCACGGCCACCGATAATAGTTTCTGAGTTTCGGAATGAGATAT ATGATGTAAGACACAGAGCTGCTTATCATCCAGACTTTCCAACAGTTCTG ACAGCTTTAGAAATAGATAATGCGGTTGTGGCAAATAGCCTAATTGACAT GAGAGGCATAGAGACAGTGCTACTAATCAAAAATAATTCTGTAGCTCGTG CAGTAATGCAGTCCCAAAAGCCACCCAAAAATTGTAGAGAAGCTTTTACT GCTGATGGTGATCAAGTTTTTGCAGGACGTTATTATTCATCTGAAAATAC AAGACCTAAGTTCCTAAGCAGAGATGTGGATTCTGAAATAAGTGACTTGG AGAATGAGGTTGAAAATAAGACGGCCCAGATATTAAATCTTCAGCAACAT TTATCTGCCCTTGAAAAAGATATTAAACACAATGAGGAACTTCTTAAAAG GTGCCAACTACATTATAAAGAACTAAAGATGAAAATAAGAAAAAATATTT CTGAAATTCGGGAACTTGAGAACATAGAAGAACACCAGTCTGTAGATATT GCAACTTTGGAAGATGAAGCTCAGGAAAATAAAAGCAAAATGAAAATGGT TGAGGAACATATGGAGCAACAAAAAGAAAATATGGAGCATCTTAAAAGTC TGAAAATAGAAGCAGAAAATAAGTATGATGCAATTAAATTCAAAATTAAT CAACTATCGGAGCTAGCAGACCCACTTAAGGATGAATTAAACCTTGCTGA TTCTGAAGTGGATAACCAAAAACGAGGGAAACGACATTATGAAGAAAAAC AAAAAGAACACTTGGATACCTTAAAAAAAAAAAAAAA
Gene structure information
H-Inv cluster ID
HIX0001845
Genomic location
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
SMC6
;
*GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links
H-DBAS
;
G-integra
;
cDNA-genome alignment
;
Predicted CDS information
HIP ID
HIP000017673
Predicted CDS
3..1087; 361[aa]; Orientation:+3;
Codon Adaptation Index (CAI).
0.662
KTDRLKRFGPNVPALLEAIDDAYRQGHFTYKPVGPLGACIHLRDPELALA IESCLKGLLQAYCCHNHADERVLQALMKRFYLPGTSRPPIIVSEFRNEIY DVRHRAAYHPDFPTVLTALEIDNAVVANSLIDMRGIETVLLIKNNSVARA VMQSQKPPKNCREAFTADGDQVFAGRYYSSENTRPKFLSRDVDSEISDLE NEVENKTAQILNLQQHLSALEKDIKHNEELLKRCQLHYKELKMKIRKNIS EIRELENIEEHQSVDIATLEDEAQENKSKMKMVEEHMEQQKENMEHLKSL KIEAENKYDAIKFKINQLSELADPLKDELNLADSEVDNQKRGKRHYEEKQ KEHLDTLKKKK
Motif information
a.a.
length
InterPro
Name
361
IPR027132
Structural maintenance of chromosomes protein 6 [Family]
Gene function information
H-Inv ID
HIT000090726
H-Inv cluster ID
HIX0001845
Accession number
BC022998.1
CAGE tag ID
NA
EST ID
NA
Transcript feature
NO;
Coding potential
Protein coding;
Definition
Similar to Structural maintenance of chromosomes protein 6.
Similarity category
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
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)
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
SMC6
;
*GeneCards is provided free to academic non-profit institutions.
etc
Human-Gene diversity Of Life-style related Diseases
;
Curation status
Auto-annotated
Notes
NA
Related H-InvDB links
Gene family;
Similarity Search Tool;
TACT
;
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;
JRE-1.4.0 or later is required.
Download JRE at
Sun's web site.
Gene expression information
Last modified:27-May-2015
Tissue-specific expression
NA
Probe
information
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-ANGEL
;
DNAProbeLocator
;
Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information
Single Nucleotide Polymorphism (SNP) and indel
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
No data available
Database links
Human-Gene diversity Of Life-style related Diseases(H-GOLD)
;
Related H-InvDB links
VaryGene
;
Repeat Mask Viewer
;