Human Gene TENT4A (ENST00000230859.8_8) from GENCODE V47lift37
  Description: terminal nucleotidyltransferase 4A, transcript variant 1 (from RefSeq NM_006999.6)
Gencode Transcript: ENST00000230859.8_8
Gencode Gene: ENSG00000112941.14_13
Transcript (Including UTRs)
   Position: hg19 chr5:6,713,545-6,757,157 Size: 43,613 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr5:6,714,097-6,755,058 Size: 40,962 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:6,713,545-6,757,157)mRNA (may differ from genome)Protein (792 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PAPD7_HUMAN
DESCRIPTION: RecName: Full=DNA polymerase sigma; EC=2.7.7.7; AltName: Full=DNA polymerase kappa; AltName: Full=LAK-1; AltName: Full=PAP-associated domain-containing protein 7; AltName: Full=Terminal uridylyltransferase 5; Short=TUTase 5; AltName: Full=Topoisomerase-related function protein 4-1; Short=TRF4-1;
FUNCTION: DNA polymerase, probably involved in DNA repair. May play a role in sister chromatid cohesion. Does not play a role in replication-dependent histone mRNA degradation.
CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
COFACTOR: Magnesium or manganese (By similarity).
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Belongs to the DNA polymerase type-B-like family.
SIMILARITY: Contains 1 PAP-associated domain.
SEQUENCE CAUTION: Sequence=AAD45198.1; Type=Frameshift; Positions=474;
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pols/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  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: 21.42 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 575.11 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 -349.00552-0.632 Picture PostScript Text
3' UTR -652.802099-0.311 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
IPR002934 - Nucleotidyltransferase
IPR002058 - PAP_assoc

Pfam Domains:
PF01909 - Nucleotidyltransferase domain
PF03828 - Cid1 family poly A polymerase
PF19088 - TUTase nucleotidyltransferase domain

SCOP Domains:
81631 - PAP/OAS1 substrate-binding domain
81301 - Nucleotidyltransferase

ModBase Predicted Comparative 3D Structure on Q5XG87
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 orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004652 polynucleotide adenylyltransferase activity
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0043221 SMC family protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006302 double-strand break repair
GO:0006397 mRNA processing
GO:0007062 sister chromatid cohesion
GO:0007076 mitotic chromosome condensation
GO:0042493 response to drug

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0031965 nuclear membrane


-  Descriptions from all associated GenBank mRNAs
  JD516440 - Sequence 497464 from Patent EP1572962.
JD189481 - Sequence 170505 from Patent EP1572962.
JD056228 - Sequence 37252 from Patent EP1572962.
JD056229 - Sequence 37253 from Patent EP1572962.
JD056230 - Sequence 37254 from Patent EP1572962.
KC424495 - Homo sapiens PAPD7 (PAPD7) mRNA, complete cds.
AF089896 - Homo sapiens topoisomerase-related function protein (TRF4-1) mRNA, partial cds.
BC084567 - Homo sapiens polymerase (DNA directed) sigma, mRNA (cDNA clone MGC:99645 IMAGE:6380576), complete cds.
AB005754 - Homo sapiens mRNA for LAK-1, complete cds.
AK289857 - Homo sapiens cDNA FLJ76751 complete cds, highly similar to Homo sapiens polymerase (DNA directed) sigma (POLS), mRNA.
BC117137 - Homo sapiens polymerase (DNA directed) sigma, mRNA (cDNA clone MGC:150746 IMAGE:40125688), complete cds.
BC126106 - Homo sapiens polymerase (DNA directed) sigma, mRNA (cDNA clone MGC:161384 IMAGE:8991822), complete cds.
BC143882 - Homo sapiens polymerase (DNA directed) sigma, mRNA (cDNA clone MGC:177415 IMAGE:9052398), complete cds.
HQ258305 - Synthetic construct Homo sapiens clone IMAGE:100072614 PAP associated domain containing 7 (PAPD7) gene, encodes complete protein.
KJ893211 - Synthetic construct Homo sapiens clone ccsbBroadEn_02605 PAPD7 gene, encodes complete protein.
KJ898338 - Synthetic construct Homo sapiens clone ccsbBroadEn_07732 PAPD7 gene, encodes complete protein.
AK308405 - Homo sapiens cDNA, FLJ98353.
AK303516 - Homo sapiens cDNA FLJ58414 complete cds, highly similar to DNA polymerase sigma (EC 2.7.7.7).
DQ596168 - Homo sapiens piRNA piR-34234, complete sequence.
JD493921 - Sequence 474945 from Patent EP1572962.
JD186516 - Sequence 167540 from Patent EP1572962.
JD243825 - Sequence 224849 from Patent EP1572962.
JD478969 - Sequence 459993 from Patent EP1572962.
JD538417 - Sequence 519441 from Patent EP1572962.
JD037215 - Sequence 18239 from Patent EP1572962.
JD496537 - Sequence 477561 from Patent EP1572962.
JD163031 - Sequence 144055 from Patent EP1572962.
JD344790 - Sequence 325814 from Patent EP1572962.
JD294951 - Sequence 275975 from Patent EP1572962.
JD545958 - Sequence 526982 from Patent EP1572962.
JD170769 - Sequence 151793 from Patent EP1572962.
JD103480 - Sequence 84504 from Patent EP1572962.
JD210986 - Sequence 192010 from Patent EP1572962.
JD075952 - Sequence 56976 from Patent EP1572962.
JD314367 - Sequence 295391 from Patent EP1572962.
JD204953 - Sequence 185977 from Patent EP1572962.
JD348321 - Sequence 329345 from Patent EP1572962.
JD196052 - Sequence 177076 from Patent EP1572962.
JD212884 - Sequence 193908 from Patent EP1572962.
JD305911 - Sequence 286935 from Patent EP1572962.

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

Protein Q5XG87 (Reactome details) participates in the following event(s):

R-HSA-6802927 BRAF and RAF fusion mutant dimers are phosphorylated
R-HSA-6802934 p-BRAF and RAF fusion dimers bind MAP2Ks and MAPKs
R-HSA-6802932 Dissociation of BRAF/RAF fusion complex
R-HSA-6802933 p-BRAF and RAF fusion dimers phosphorylate MAP2Ks
R-HSA-6802935 MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers
R-HSA-6802952 Signaling by BRAF and RAF fusions
R-HSA-6802957 Oncogenic MAPK signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A0A0X1KG68, A8K1E2, ENST00000230859.1, ENST00000230859.2, ENST00000230859.3, ENST00000230859.4, ENST00000230859.5, ENST00000230859.6, ENST00000230859.7, M1JCE6, NM_006999, O43289, PAPD7 , PAPD7_HUMAN, POLS , Q17RZ1, Q5XG87, Q9Y6C1, TENT4A , TRF4 , uc317dtj.1, uc317dtj.2
UCSC ID: ENST00000230859.8_8
RefSeq Accession: NM_006999.6
Protein: Q5XG87 (aka PAPD7_HUMAN)

-  Gene Model Information
  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.