Human Gene SSU72 (uc001agd.3) Description and Page Index
  Description: Homo sapiens SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) (SSU72), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:1,477,053-1,510,262 Size: 33,210 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr1:1,477,446-1,509,937 Size: 32,492 Coding Exon Count: 5 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:1,477,053-1,510,262)mRNA (may differ from genome)Protein (194 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SSU72_HUMAN
DESCRIPTION: RecName: Full=RNA polymerase II subunit A C-terminal domain phosphatase SSU72; Short=CTD phosphatase SSU72; EC=3.1.3.16;
FUNCTION: May be involved in the C-terminal domain of RNA polymerase II dephosphorylation, RNA processing and termination.
CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate.
SUBUNIT: Interacts with RB1. Interacts with GTF2B and CD226.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Predominantly in the cytosol.
SIMILARITY: Belongs to the SSU72 phosphatase family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SSU72
CDC HuGE Published Literature: SSU72
Positive Disease Associations: Glucose
Related Studies:
  1. Glucose
    , , . [PubMed 0]
  2. Glucose
    , , . [PubMed 0]
  3. Glucose
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.35 RPKM in Thyroid
Total median expression: 1436.68 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 -185.60325-0.571 Picture PostScript Text
3' UTR -113.50393-0.289 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
IPR006811 - RNA_pol_II_suA

Pfam Domains:
PF04722 - Ssu72-like protein

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3O2Q
- X-ray MuPIT

3O2S
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9NP77
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:0004721 phosphoprotein phosphatase activity
GO:0005515 protein binding
GO:0008420 CTD phosphatase activity
GO:0016787 hydrolase activity

Biological Process:
GO:0006369 termination of RNA polymerase II transcription
GO:0006378 mRNA polyadenylation
GO:0006397 mRNA processing
GO:0070940 dephosphorylation of RNA polymerase II C-terminal domain

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex


-  Descriptions from all associated GenBank mRNAs
  AF161530 - Homo sapiens HSPC182 mRNA, complete cds.
BC008070 - Homo sapiens SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae), mRNA (cDNA clone MGC:2805 IMAGE:2961422), complete cds.
BC018909 - Homo sapiens SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4054323).
AK127149 - Homo sapiens cDNA FLJ45206 fis, clone BRCAN2010581.
AK001809 - Homo sapiens cDNA FLJ10947 fis, clone PLACE1000066, weakly similar to SSU72 PROTEIN.
AJ276409 - Homo sapiens mRNA for hypothetical protein, clone STRAIT14513.
JD399838 - Sequence 380862 from Patent EP1572962.
JD450481 - Sequence 431505 from Patent EP1572962.
AF277178 - Homo sapiens PNAS-120 mRNA, complete cds.
JD084111 - Sequence 65135 from Patent EP1572962.
DQ892987 - Synthetic construct clone IMAGE:100005617; FLH191433.01X; RZPDo839D0277D SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) (SSU72) gene, encodes complete protein.
DQ896236 - Synthetic construct Homo sapiens clone IMAGE:100010696; FLH191429.01L; RZPDo839D0267D SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) (SSU72) gene, encodes complete protein.
AK310067 - Homo sapiens cDNA, FLJ17109.
AK297505 - Homo sapiens cDNA FLJ60055 complete cds, highly similar to Rattus norvegicus Ssu72 RNA polymerase II CTD phosphatase homolog, mRNA.
AK023110 - Homo sapiens cDNA FLJ13048 fis, clone NT2RP3001399, weakly similar to SSU72 PROTEIN.
AK291324 - Homo sapiens cDNA FLJ77664 complete cds.
JD129653 - Sequence 110677 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: HSPC182, NM_014188, NP_054907, PNAS-120, Q9BZS6, Q9H933, Q9NP77, SSU72_HUMAN
UCSC ID: uc001agd.3
RefSeq Accession: NM_014188
Protein: Q9NP77 (aka SSU72_HUMAN)
CCDS: CCDS32.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014188.2
exon count: 5CDS single in 3' UTR: no RNA size: 1319
ORF size: 585CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1370.00frame shift in genome: no % Coverage: 98.79
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.