Human Gene SMUG1 (uc009znf.2) Description and Page Index
  Description: Homo sapiens single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1), transcript variant 3, mRNA.
RefSeq Summary (NM_001243788): This gene encodes a protein that participates in base excision repair by removing uracil from single- and double-stranded DNA. Many alternatively spliced transcript variants exist for this gene; the full-length nature is known for some but not all of the variants. [provided by RefSeq, Aug 2011]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1803617.155206.1, SRR1803617.196755.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: hg19 chr12:54,574,142-54,582,778 Size: 8,637 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr12:54,575,880-54,577,724 Size: 1,845 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:54,574,142-54,582,778)mRNA (may differ from genome)Protein (270 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SMUG1_HUMAN
DESCRIPTION: RecName: Full=Single-strand selective monofunctional uracil DNA glycosylase; EC=3.2.2.-;
FUNCTION: Responsible for recognizing base lesions in the genome and initiating base excision DNA repair. Acts as a monofunctional DNA glycosylase specific for uracil (U) residues in DNA and has a preference for single-stranded DNA substrates. The activity is greater against mismatches (U/G) than against matches (U/A). Excised uracil (U), 5-formyluracil (fU) and uracil derivatives bearing an oxidized group at C5 [5-hydroxyuracil (hoU) and 5- hydroxymethyluracil (hmU)] in ssDNA and dsDNA but not analogous cytosine derivatives (5-hydroxycytosine and 5-formylcytosine) and other oxidized damage. The activity is damage specificity and salt concentration-dependent. The general order of the preference for ssDNA and dsDNA is the following: ssDNA > dsDNA (G pair) = dsDNA (A pair) at the low salt concentration. At the high concentration dsDNA (G pair) > dsDNA (A pair) > ssDNA.
INTERACTION: Q93062:RBPMS; NbExp=2; IntAct=EBI-749970, EBI-740322;
SUBCELLULAR LOCATION: Nucleus.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/smug1/";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SMUG1
CDC HuGE Published Literature: SMUG1

-  MalaCards Disease Associations
  MalaCards Gene Search: SMUG1
Diseases sorted by gene-association score: rectosigmoid junction neoplasm (19), bone lymphoma (16), extratemporal epilepsy (16), baastrup's syndrome (16), plexopathy (15), prostate neuroendocrine neoplasm (15), lower gum cancer (15), rectum squamous cell carcinoma (14), gummatous syphilis (14), chest wall lipoma (14), small intestine leiomyoma (14), malignant ovarian brenner tumor (14), uterine corpus sarcoma (14), renal pelvis squamous cell carcinoma (14), localized chondrosarcoma (14), retroperitoneal hemangiopericytoma (14), trachea squamous cell carcinoma (14), splenic tuberculosis (13), central nervous system vasculitis (12), aortitis (12), pediatric lymphoma (11), breast lymphoma (11), mediastinal cancer (11), mikulicz disease (11), skeletal tuberculosis (10), simultanagnosia (10), alzheimer disease 16 (10), pulmonary artery leiomyosarcoma (10), sternum cancer (10), cardiovascular syphilis (10), supraglottis cancer (10), tibial adamantinoma (10), liver lymphoma (10), gallbladder squamous cell carcinoma (10), pleural cancer (9), cardiac sarcoidosis (9), xanthogranulomatous cholecystitis (9), cecal benign neoplasm (9), thymus cancer (9), prostatic cyst (8), parapharyngeal meningioma (8), spinal cord melanoma (8), trachea adenoid cystic carcinoma (8), bladder calculus (8), tracheal cancer (8), gum cancer (8), extragonadal nonseminomatous germ cell tumor (8), breast leiomyosarcoma (8), hypersensitivity reaction type iv disease (8), hypopharynx cancer (8), temporal arteritis (8), heart cancer (8), lemierre's syndrome (7), pericardium cancer (7), cerebral lymphoma (7), malignant skin fibrous histiocytoma (7), malignant dermis tumor (7), prostate squamous cell carcinoma (7), pancoast tumor (7), cortical deafness (7), corpus luteum cyst (7), partial motor epilepsy (7), cellular ependymoma (7), bartholin's duct cyst (7), schneiderian carcinoma (7), actinomycosis (7), extragonadal germ cell cancer (7), brain sarcoma (7), gastrointestinal tuberculosis (7), eccrine adenocarcinoma (7), malignant spiradenoma (7), hepatic tuberculosis (7), adult lymphoma (6), anthracosilicosis (6), prostate lymphoma (6), pharynx cancer (6), ovarian carcinosarcoma (6), hemangioma of spleen (6), bone epithelioid hemangioma (6), ascending colon cancer (6), oropharynx cancer (6), cell type cancer (6), lung lymphoma (6), non-secretory myeloma (6), tuberculous peritonitis (6), endocardium disease (6), abdominal tuberculosis (6), chondromalacia (6), klatskin's tumor (6), heart sarcoma (6), pericardial tuberculosis (6), benign struma ovarii (5), gallbladder small cell carcinoma (5), gastric signet ring cell adenocarcinoma (5), rectal neoplasm (5), gastrointestinal neuroendocrine tumor (5), extraosseous osteosarcoma (5), pulmonary alveolar microlithiasis (5), tolosa-hunt syndrome (5), appendix adenocarcinoma (5), anus cancer (5), cecum adenocarcinoma (5), xanthogranulomatous pyelonephritis (5), dissociative amnesia (5), jejunal adenocarcinoma (5), oculomotor nerve paralysis (5), third cranial nerve disease (5), mature teratoma (5), retroperitoneal leiomyosarcoma (5), anomalous left coronary artery from the pulmonary artery (5), nervous system benign neoplasm (5), scrotal carcinoma (5), corneal endothelial dystrophy, autosomal recessive (5), pulmonary aspergilloma (5), eumycotic mycetoma (5), ectopic cushing syndrome (5), secondary hypertrophic osteoarthropathy (5), intermittent explosive disorder (5), laryngeal tuberculosis (5), testicular leydig cell tumor (5), granulomatous myositis (5), femoral neuropathy (5), in situ pulmonary adenocarcinoma (5), endometrial small cell carcinoma (4), visual agnosia (4), n syndrome (4), pericardial mesothelioma (4), testis seminoma (4), cervical adenosquamous carcinoma (4), hemidystonia (4), nominal aphasia (4), alzheimer disease-2 (4), lipid pneumonia (3), kleine-levin hibernation syndrome (3), cogan syndrome (3), speech and communication disorders (2), endocrine gland cancer (2), gastrointestinal system cancer (2), connective tissue cancer (1), female reproductive organ cancer (1), dementia, lewy body (1), reproductive organ cancer (1), dementia, frontotemporal (1), nervous system disease (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 7.13 RPKM in Prostate
Total median expression: 254.03 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -13.7063-0.217 Picture PostScript Text
3' UTR -568.901738-0.327 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
IPR005122 - Uracil-DNA_glycosylase-like

SCOP Domains:
52141 - DNA glycosylase

ModBase Predicted Comparative 3D Structure on Q53HV7
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
GO:0003677 DNA binding
GO:0004844 uracil DNA N-glycosylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0017065 single-strand selective uracil DNA N-glycosylase activity
GO:0019104 DNA N-glycosylase activity

Biological Process:
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006974 cellular response to DNA damage stimulus
GO:0045008 depyrimidination

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  AK091468 - Homo sapiens cDNA FLJ34149 fis, clone FCBBF3012588, highly similar to Homo sapiens single-strand selective monofunctional uracil DNA glycosylase mRNA.
AX747003 - Sequence 528 from Patent EP1308459.
BC088352 - Homo sapiens single-strand-selective monofunctional uracil-DNA glycosylase 1, mRNA (cDNA clone MGC:110989 IMAGE:6470294), complete cds.
AK001789 - Homo sapiens cDNA FLJ10927 fis, clone OVARC1000466.
AK001235 - Homo sapiens cDNA FLJ10373 fis, clone NT2RM2001935.
AF125182 - Homo sapiens single-strand selective monofunctional uracil DNA glycosylase mRNA, complete cds.
BC000417 - Homo sapiens single-strand-selective monofunctional uracil-DNA glycosylase 1, mRNA (cDNA clone MGC:8633 IMAGE:2961516), complete cds.
BC105607 - Homo sapiens single-strand-selective monofunctional uracil-DNA glycosylase 1, mRNA (cDNA clone MGC:104370 IMAGE:6724466), complete cds.
CU674206 - Synthetic construct Homo sapiens gateway clone IMAGE:100017971 5' read SMUG1 mRNA.
KJ902356 - Synthetic construct Homo sapiens clone ccsbBroadEn_11750 SMUG1 gene, encodes complete protein.
KU178578 - Homo sapiens single-strand-selective monofunctional uracil-DNA glycosylase 1 isoform 1 (SMUG1) mRNA, partial cds, alternatively spliced.
KU178579 - Homo sapiens single-strand-selective monofunctional uracil-DNA glycosylase 1 isoform 2 (SMUG1) mRNA, complete cds.
JD355909 - Sequence 336933 from Patent EP1572962.
JD073496 - Sequence 54520 from Patent EP1572962.
JD531359 - Sequence 512383 from Patent EP1572962.
JD282474 - Sequence 263498 from Patent EP1572962.
JD092239 - Sequence 73263 from Patent EP1572962.
AK290274 - Homo sapiens cDNA FLJ77802 complete cds, highly similar to Homo sapiens single-strand selective monofunctional uracil DNA glycosylase (SMUG1), mRNA.
JD235995 - Sequence 217019 from Patent EP1572962.
JD428182 - Sequence 409206 from Patent EP1572962.
JD528109 - Sequence 509133 from Patent EP1572962.
JD291231 - Sequence 272255 from Patent EP1572962.
JD060401 - Sequence 41425 from Patent EP1572962.
JD186574 - Sequence 167598 from Patent EP1572962.
JD556799 - Sequence 537823 from Patent EP1572962.
AK222473 - Homo sapiens mRNA for single-strand selective monofunctional uracil DNA glycosylase variant, clone: adKA01737.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03410 - Base excision repair

Reactome (by CSHL, EBI, and GO)

Protein Q53HV7 (Reactome details) participates in the following event(s):

R-HSA-110164 SMUG1 glycosylase mediated recognition and binding of uracil in DNA
R-HSA-110351 Displacement of SMUG1 glycosylase by APEX1 at the AP site
R-HSA-110221 Cleavage of uracil by SMUG1 glycosylase
R-HSA-110328 Recognition and association of DNA glycosylase with site containing an affected pyrimidine
R-HSA-110357 Displacement of DNA glycosylase by APEX1
R-HSA-110329 Cleavage of the damaged pyrimidine
R-HSA-73928 Depyrimidination
R-HSA-73933 Resolution of Abasic Sites (AP sites)
R-HSA-73929 Base-Excision Repair, AP Site Formation
R-HSA-73884 Base Excision Repair
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: A8K2K9, NM_001243788, NP_055126, O95862, Q0D2M0, Q53HV7, Q8NB71, Q9BWC8, SMUG1_HUMAN
UCSC ID: uc009znf.2
RefSeq Accession: NM_001243788
Protein: Q53HV7 (aka SMUG1_HUMAN)
CCDS: CCDS8874.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001243788.1
exon count: 3CDS single in 3' UTR: no RNA size: 2632
ORF size: 813CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1697.00frame shift in genome: no % Coverage: 99.32
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 2146# 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.