Human Gene SMC5 (uc004ahr.2) Description and Page Index
  Description: Homo sapiens structural maintenance of chromosomes 5 (SMC5), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:72,873,878-72,969,789 Size: 95,912 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr9:72,873,995-72,967,247 Size: 93,253 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:72,873,878-72,969,789)mRNA (may differ from genome)Protein (1101 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
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neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SMC5_HUMAN
DESCRIPTION: RecName: Full=Structural maintenance of chromosomes protein 5; Short=SMC protein 5; Short=SMC-5; Short=hSMC5;
FUNCTION: Core component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs). Required for recruitment of telomeres to PML nuclear bodies. Required for sister chromatid cohesion during prometaphase and mitotic progression; the function seems to be independent of SMC6.
SUBUNIT: Forms a heterodimer with SMC6. Component of the SMC5-SMC6 complex which consists at least of SMC5, SMC6, NSMCE2, NSMCE1, NSMCE4A or EID3 and NDNL2.
INTERACTION: Q96SB8:SMC6; NbExp=3; IntAct=EBI-605405, EBI-605415;
SUBCELLULAR LOCATION: Nucleus. Chromosome. Chromosome, telomere. Note=Associates with chromatin. Localizes to PML nuclear bodies in ALT cell lines.
TISSUE SPECIFICITY: Widely expressed.
DOMAIN: The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of SMC6, forming a V- shaped heterodimer (By similarity).
PTM: Sumoylated.
PTM: Ubiquitinated.
SIMILARITY: Belongs to the SMC family. SMC5 subfamily.
SEQUENCE CAUTION: Sequence=AAH17666.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SMC5
CDC HuGE Published Literature: SMC5
Positive Disease Associations: Body Mass Index , Hip
Related Studies:
  1. Body Mass Index
    Yukinori Okada et al. Nature genetics 2012, Common variants at CDKAL1 and KLF9 are associated with body mass index in east Asian populations., Nature genetics. [PubMed 22344221]
  2. Hip
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.
  3. Hip
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.
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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.49 RPKM in Ovary
Total median expression: 379.82 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -58.10117-0.497 Picture PostScript Text
3' UTR -587.142542-0.231 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003395 - RecF/RecN/SMC

Pfam Domains:
PF02463 - RecF/RecN/SMC N terminal domain
PF13175 - AAA ATPase domain
PF13476 - AAA domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q8IY18
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005515 protein binding
GO:0005524 ATP binding

Biological Process:
GO:0000722 telomere maintenance via recombination
GO:0000724 double-strand break repair via homologous recombination
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006974 cellular response to DNA damage stimulus
GO:0007049 cell cycle
GO:0007062 sister chromatid cohesion
GO:0034184 positive regulation of maintenance of mitotic sister chromatid cohesion
GO:0051301 cell division
GO:0051984 positive regulation of chromosome segregation
GO:0090398 cellular senescence
GO:0006303 double-strand break repair via nonhomologous end joining

Cellular Component:
GO:0000781 chromosome, telomeric region
GO:0000803 sex chromosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0016605 PML body
GO:0016607 nuclear speck
GO:0030054 cell junction
GO:0030915 Smc5-Smc6 complex
GO:0035061 interchromatin granule
GO:0035861 site of double-strand break


-  Descriptions from all associated GenBank mRNAs
  AK304133 - Homo sapiens cDNA FLJ61059 complete cds, highly similar to Homo sapiens SMC5 structural maintenance of chromosomes 5-like 1 (SMC5L1), mRNA.
BC038225 - Homo sapiens structural maintenance of chromosomes 5, mRNA (cDNA clone MGC:40432 IMAGE:5417143), complete cds.
BC017666 - Homo sapiens structural maintenance of chromosomes 5, mRNA (cDNA clone IMAGE:3913418), partial cds.
AB011166 - Homo sapiens KIAA0594 mRNA for KIAA0594 protein.
AK055825 - Homo sapiens cDNA FLJ31263 fis, clone KIDNE2006009, weakly similar to HYPOTHETICAL 122.9 KDA PROTEIN C14C4.02 IN CHROMOSOME I.
AB385355 - Synthetic construct DNA, clone: pF1KA0594, Homo sapiens SMC5 gene for structural maintenance of chromosomes protein 5, complete cds, without stop codon, in Flexi system.
DQ896768 - Synthetic construct Homo sapiens clone IMAGE:100011228; FLH196617.01L; RZPDo839F11155D structural maintenance of chromosomes 5 (SMC5) gene, encodes complete protein.
DQ893364 - Synthetic construct clone IMAGE:100005994; FLH196621.01X; RZPDo839F11156D structural maintenance of chromosomes 5 (SMC5) gene, encodes complete protein.
AJ310550 - Homo sapiens mRNA for SMC5 protein.
JD360379 - Sequence 341403 from Patent EP1572962.
BC034441 - Homo sapiens structural maintenance of chromosomes 5, mRNA (cDNA clone IMAGE:4519250).
JD541312 - Sequence 522336 from Patent EP1572962.
JD542301 - Sequence 523325 from Patent EP1572962.
JD333302 - Sequence 314326 from Patent EP1572962.
JD341403 - Sequence 322427 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8IY18 (Reactome details) participates in the following event(s):

R-HSA-3108212 SMC5-SMC6 Complex SUMOylates Cohesin with SUMO1
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-2990846 SUMOylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A6NM81, KIAA0594, NM_015110, NP_055925, O60335, Q05D92, Q5VZ60, Q8IY18, Q96SB9, SMC5L1, SMC5_HUMAN
UCSC ID: uc004ahr.2
RefSeq Accession: NM_015110
Protein: Q8IY18 (aka SMC5_HUMAN)
CCDS: CCDS6632.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015110.3
exon count: 25CDS single in 3' UTR: no RNA size: 5965
ORF size: 3306CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6613.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.