Gene detail

Detailed information of ENSDKPP00000010063.1 in Plumapathes pennacea

Genomic Location: chr10:6164874...6178306
NR annotation: XP_022789866.1, DNA polymerase beta-like isoform X1 [Stylophora pistillata]
Species Plumapathes pennacea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSDKPT00000010063

CGTTGACGCGCAAAAAAAGAAGCAGAACACGGCTGTATTGCTGGCTTTCCAAGGTTCAGCCTGCTTTTTCCTCTTCTCTGTTTGGCTTGATTTGTGCAGCACGCACTTTCAAACCACAGCAAGGTTCCTGTAATACTGAATTGGTGACGTAAAGAAAATCCAATCGATAATTATTCGGAATCAATTCGGATAATAGATCCCAGGCTTCTGTGAGGTCGAGGGCGCGTGATACGAGAATCATGAGCAAACGAAAAGCGGTTGAGCAAAATCCAAACTCCGAGTTCTGCGAGTTTTTGACAGAGCTTGCAGAACACGAGAAGAATGTATCAAGACAAATCCATAAATACAATGCTTACAGGAAAGCAGCAGCTGCCCTTGCTAAACATCCAACAAAAATAGCAAGTGGAGAAGAGGCCAAGAAACTGCCTGGCATTGGGGATAAAATTGCCAAGAAAATATCTGAGTTCATCAAAACAGGGAAGCTTGAGAAACTAGAGAAGATAAGGGCAGATGATACCAGCCAGGCCATAAAAGAACTCACCAGGGTTTCAGGAATTGGcccTGCAGCCGCCAGAAAGTTTGTGGAAGAAGGAGTGACAACTATACAAGacTTACGGAAGGTAGAGGGACAACTGAACCATCATCAAAAGATTGGTCTGAAGTATCTAGAGGATTTTGAAAAACGCATACCAAGGGAGGAAATGCTGCAACTGCAGGAAGTCGTCCTTCGAGAAGTTCAAAGACATGATAGCGATCTCGTGGCCACAATCTGTGGCAGCTTCCGGAGAGGGGCTGCTTCCAGTGGCGACATCGATGTACTTGTCACGCATCCTTCCTTTGTGTCGACAGAGAAGAAATTCGACAAGAAGTCCCTGCTGCAGGGTGTAGTGAACAAGATGAAAGAAGCCAAGTTTGTGACAGACACGTTGTCCCAAGGAGAAACCAAATTCATGGGTGTATGTTCTCTCTCTAAAGAGAGGATAGGAGAGAGTTTGTACAGGAGGATTGATATCAGACTCATTCCCTGTGATCAGTACTACTGTGGCATTCTGTACTTCACTGGAAGTGACGAGTTTAACAGACAGATGAGGCAGCAGGCCCTCGATAAAGGATTCACTCTCAACGAATACTGCATCAGGCCTCTCGGAAGTACAGGTGTTCCCGGAGAATCCATTCCAGTGTCAAGTGAAGAAGAAGTATTCAACGCTATTGGAATGGACTACAAAGCTCCACAAGAACGGAATGTGTGATTATTGTCACCCCGTGCAACCAGTCCATCCTGGAGTTCATAGGTACTACTAACACAAAGTAACGTAAACTGACACAACCTGGTACGACTTTTGCGAAAGACCTCAAGAACAAGATATATCGATTagtataaacaacaacaacaataataacattaAACTGGTGAGGTACCTCTCAACCACACTCCTTTGCACGCTGGGAATCCTCGACCTGCCATTTTCATGGCTGGTCCAGAACGTCGAAAAGCAAATTGGCAACCAGTTCTATCTTCAGTTCTCCTTTAAGCAATAATTGCAAGGTCACACGATAAGAGGATAACCATTTGGTTTTGAGCACATCGTCCACATCCAATCAGTTTCTAGTTGTTTCATTTCAGCTCCCTTTTAACTCCGGTGTTTTATGGTATTTTGCAATTTGTGTACGCAATTTATGTACGCTAGGTCATTTGTGCACACCGTACAAATCTCCACAAAACCCAACTCACCCGCTTGGTCTTTGCAGTTGGAaggtttgaaaatattttccGATCACGTGTACCTTCGCcctgtaattttttttattttaaagtaCGCacataaaagcaaaatatttccatACCAGTATGACTTCCGGTATGTTTTGATTGGCTCATTTTGCGCAATGTGACAGGCATTCCTTTCTCCCGCACCCGTTTTGTCACGGAACGCCTGCTTTTCACAAGATTCCGGTTGATTGATTTCGGACAGTTGATTGGTTCTGTGAGTCCCCATGAGACTGACGTCACGATAAATTTCACAAGTTTACGGCATTTGCAATACACGAGGTGGAAGACGCGTCCATTTGCTTCGGGACGCTTTAGAGTGTGGATGTGCGACCAGGCTGTGTGAGTGCAGGTACTTTTCCAGTTTGATATCCTGGAACGCCTTTT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q27958	DNA polymerase beta OS=Bos taurus OX=9913 GN=POLB PE=2 SV=3
Q8K409	DNA polymerase beta OS=Mus musculus OX=10090 GN=Polb PE=1 SV=3
P06746	DNA polymerase beta OS=Homo sapiens OX=9606 GN=POLB PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001967 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10391 all species →	DNA_pol_lambd_f	Fingers domain of DNA polymerase lambda	Domain	Interproscan
PF14716 all species →	HHH_8	Helix-hairpin-helix domain	Domain	Interproscan
PF14792 all species →	DNA_pol_B_palm	DNA polymerase beta palm	Domain	Interproscan
PF14791 all species →	DNA_pol_B_thumb	DNA polymerase beta thumb	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR043519 all species →	Homologous_superfamily	Nucleotidyltransferase superfamily	Interproscan
IPR027421 all species →	Homologous_superfamily	DNA polymerase lambda lyase domain superfamily	Interproscan
IPR018944 all species →	Domain	DNA polymerase lambda, fingers domain	Interproscan
IPR037160 all species →	Homologous_superfamily	DNA polymerase, thumb domain superfamily	Interproscan
IPR010996 all species →	Domain	DNA polymerase beta-like, N-terminal domain	Interproscan
IPR003583 all species →	Domain	Helix-hairpin-helix DNA-binding motif, class 1	Interproscan
IPR028207 all species →	Domain	DNA polymerase beta, palm domain	Interproscan
IPR002054 all species →	Domain	DNA-directed DNA polymerase X	Interproscan
IPR029398 all species →	Domain	DNA polymerase beta, thumb domain	Interproscan
IPR019843 all species →	Binding_site	DNA polymerase family X, binding site	Interproscan
IPR002008 all species →	Family	DNA polymerase family X, beta-like	Interproscan
IPR022312 all species →	Family	DNA polymerase family X	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11276 all species →	DNA POLYMERASE TYPE-X FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0034061 all species →	Molecular Function	DNA polymerase activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0016779 all species →	Molecular Function	nucleotidyltransferase activity	Interproscan
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K02330	POLB; DNA polymerase beta	EC:2.7.7.7 EC:4.2.99.-	DNA repair and recombination proteins	ko03400	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Plumapathes pennacea tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Plumapathes pennacea, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →