Gene detail

Detailed information of ENSQPTP00000007308.1 in Actinia mediterranea

Genomic Location: chr12:10143347...10162415
NR annotation: XP_031549547.1, DNA damage-binding protein 1-like [Actinia tenebrosa]
Species Actinia mediterranea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSQPTT00000009101

ATGGCTTATAACTACGTAGTCACTGCACAAAAACCTACTGCAGTGAACGCTGCGGTCGTAGGGAATTTTACGGGTCCAAATGACTTGAACCTTGTCATCGCCAAGAACACGAGAATAGAGATCCATCTCGTTACGCCAGAAGGATTGAGACCGATGCTGGATGTAGGAATATATGGACGGGTCTGCGTTATGGAGTTGTTTCGTCCTCCTAATGAGCCTCAAGACTTGCTGTTCATTCTAACGGCACGGTATAGAGTCTGTATCCTTGGATATAAACAAGAAACTGGTGATATAGTCACACGTGCATGCGGCGATGTACAAGACCGAATAGGCCGACCATCAGATACTGGTCTTATAGCAATAATAGATCCTCAGTGTCGGATGATTGGCTTGCGTCTGTATGATGGTCTGTTCAAGGTTATACCACTAGAGCTGGATTCCAGTAAAGAACTCAAGGCTTACAATATCAGACTGGAGGAGCTACATGTTATTGATATTCAATTCCTCCATGGGTGTGAAGCACCAACAATAGTGTTCATATACCAGGAAACCCATGGCCGTCATGTGAAAACTTATGAAGTAAACTTGAGAGAACATGAGTTCGTGAAAGGACCCTGGAAGCAGGATAATGTTGAAGTTGAAGCATGTAGGATTATTGCAGTCCCTGAACCTCTCTGTGGTGCACTTATCATCGGTCAAGAGTCTATTACGTACCACAAAGGATCTAATTATTATGCCATCGCACCTCCAGCACTCAAGCAAAGTACAATCAATTGCTATGGTAAGATTGATGCCAATGGATCAAGATACCTTCTAGGTGACATGAATGGACGATTATTCATGTTGCTATTGGAGAAGCAAGAACTAATGGATGGTAACATTGAGGTCAAAGATCTGAAACTTGAGCTCTTGGGAGAGACATCGATTGCTCAGTGTCTTGTATATCTGGACAATGGAGTAGTGTTTGTAGGGTCTGTTTTAGGAGACTCTCAGCTTGCCAAGTTAAATACAGAGGTTGATGCCCGTGGCTCATACGTCCAAGTCTTAGAAACGTTCACTAATCTAGGTCCAATAGTAGATATGGTCGTGGTAGACTTAGAACGGCAAGGACAAGGACAGCTTGTAACATGTTCCGGCGCAAATAAAGAAGGCTCCCTGCGCATCATTCGAAATGGCATAGGCATTCATGAGCATGCGACTATAGACCTGCCAGGAATTATGGGTATCTGGGCAATAAAACTTGATAAGACAGAGGAAGACCATGATGATACTCTTGTACTTGCTTTTGTTGGAGGAAGCAGAGTCTTGTCCTTGAATGGTGAAGAAGTAGAAGAAACAGAGATCTCTGGGTTTGATGATAATCAGCAAACTTATTTTTGTGGAAATGTTCGAGACGACCAAATTATCCAGatAACTGCTCACTCGGTAAGACTGGTGAACTGTAAAACAAGACAGCTAGTGAGtgaatggaAACATTGGTCTGGTAAGAATATCAGTGTAGCAGCATGCAATACGGAGCAAGTAGTGACTGCAGTTGGCAGTGAACTGTTCTACATCGAGATAGGACCAGGAAAACTGGAACAAATCAGCCAAGTGACTATGGAACATGAAGTTGCTTGTCTAGACATCACACCAACAGTTGACCAGAATGCCAAGGCAGATATGATTGGTGTTGGTTTGTGGACAGATATTTCTATAAGAGTACTCAGAATTCCTGATTTAGATTCTCTGTATGTGGAAATGTTGGGTGGAGAAATTATCCCTCGTTCCATCTTAAAGACTTCATTTGAAGGGATACATTACCTGCTTTGTGCTCTTGGTGATGGTACACTTTTCTACTTCAATATGGACCCACATAATGGTGTCCTATCAGAGCGTAAAAAAGTGACCTTGGGCACCCAGCCCACCATATTAAGGACCTTCAAGTCCCTGTCAACTGTGAATGTGTTTGCTTGCTCAGACAGGCCCACAGTGATTTACTCCAGTAATCACAAGCTAGTGTTCTCTAATGTCAACCTCAAGGAAGTGAATTACATGTGTCCATTAAATTCAAAAGGCTATCCAGACAGtcTTGCCCTTGCTAATGAAGGTGCCTTGACCATTGGAACTATTGATGAAATCCAAAAACTCCACATTAGGACAGTACCCTTGGGGGAATCACCAAGGCGCATAGCATATCAAGAAGCCACACAATCCTTCGGCATCGTATCAGTACGTATCGAAGTATATGAACCAAGCCAGGACAGGACTGTCCCTCTTCACCCTAGTGCTAGCTCGACAGCGAATAATATAACCTCATCTGCCAGCACCAACATGTCAGGGACATCAGAAGGGGCTTCTGGTGCTAGTCATTCTGCCGTTGATGGTATTACGTTTGGGGATGAGATTGAAGTTAGCAGTCTACTTATTGTTGACCAACACACTTTTGAAGTAACACATGCTCATCAGCTAAAAGATAATGAATGTGCTACAAGTCTGATGTCATGTACACTATCTGATGACCCTAACACATACTACTGTGTGGGAACGGCATTTGTGTTCCCTGAGGAAGCTGAACCTAAATCAGGCAGACTACTTCTCTTCCAACTAACAGAAGGTAAGCTGGTACAAGTTGCTGAAAAAGAAGTTAAGGGAGCAGTTTACAGCTTGGTTGAATTCAACGGCAAGGTCCTTGCTGGAATCAATAGCAATgTGGGGATATATGAGTGGACAGCCGACAAGGAACTAAGACAAGAGTGTTGTTACTTTGACAACATACTCGTACTCTACCTCAAAACAAAAGGGGACTTTATTCTGGTTGGTGATCTAATGCGTTCAATGACTCTTCTTGTTTATCTCCCAATGGAAGGCTCATTGCAAGAGATTGCACATGACTTCAGTCCCAAGTGGATGACTGCAGTCGAGATACTTGATGATGACACATTCCTTGGTGCCGAAAACTCATTCAACCTATTTACCTGTCAAAAGAACAGTGGAGCCACAACCGACGAAGAGAGATTCTACTTACAAGATGCTGGCCAGTATCACCTGGGCGAATTCGTGAATGTATTCAGGCATGGCTCATTGGTAATGGAACACCTAGGGGAGTCCTCCACTCCATTCCAAGGAAGCATACTATATGGCACAGTCAACGGAAGAATAGgtatcgtaggACAGCTATCTAAAGATCTCTTCGAGTTTCTCTTACAAGTTcaaaaaaagttaactaaagTCATCAAGAGTGAACTAAAGTTCATCACCATGTTATTTACTTTAACCTTGTTCACCTGGCGTTCGTTCTCAAATGAACGCAAAACAGAACCAGCGAATGGCTTTATCGATGGTGATCTGATCGAGAGTTTTCTTGACCTTCCTCGAGCTAAGATGAAGGAGGTAGCCGCTGGACTTCAGACTGACGATGGCagtggaatgaaaaaagaatgcACCGTTGAAGACCTGGTAAAGACTGTCGAGGAACTCACGCGAATTCACTAG

Transcript

ENSQPTT00000009101

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3U1J4	DNA damage-binding protein 1 OS=Mus musculus OX=10090 GN=Ddb1 PE=1 SV=2
A1A4K3	DNA damage-binding protein 1 OS=Bos taurus OX=9913 GN=DDB1 PE=1 SV=1
Q16531	DNA damage-binding protein 1 OS=Homo sapiens OX=9606 GN=DDB1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003690 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DDB1 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03178 all species →	CPSF_A	CPSF A subunit region	Repeat	Interproscan
PF10433 all species →	MMS1_N	Mono-functional DNA-alkylating methyl methanesulfonate N-term	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR004871 all species →	Domain	Cleavage/polyadenylation specificity factor, A subunit, C-terminal	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR050358 all species →	Family	RSE1/DDB1/CFT1/CPSF1	Interproscan
IPR018846 all species →	Domain	Cleavage/polyadenylation specificity factor, A subunit, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10644 all species →	DNA REPAIR/RNA PROCESSING CPSF FAMILY	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0035861 all species →	Cellular Component	site of double-strand break	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	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
K10610	DDB1; DNA damage-binding protein 1	-	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 Actinia mediterranea 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 Actinia mediterranea, 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 →