Gene detail

Detailed information of ENSOJPP00000033324.1 in Anthopleura xanthogrammica

Genomic Location: chr1:23021629...23035604
NR annotation: XP_031565707.1, general transcription and DNA repair factor IIH helicase subunit XPB-like [Actinia tenebrosa]
Species Anthopleura xanthogrammica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSOJPT00000038595

TATGGATCTGAAACCAACAACTGTTCTAAGGCCATATCAGGAGAAAAGTCTGAGAAAGATGTTTGGCAATGGACGAGCGCGTTCTGGAGTTATCGTCCTACCGTGTGGTGCTGGTAAGACTCTAGTGGGTGTAACTGCTGCATGTACGGTTAGGAAGCCATGCCTCATTCTCTGCACTTCAGGTGTTGCTGTTGAGCAATGGCGCAGTCAGTTCAAGCTTTGGTCAACTGTTGACAGTCGAATCATATGTTGTTTCACATCAGATGCTAAAGATAAACCAAAAGATTGTGGGATAGCTATTTCTACGTATTCAATGGTGTCACATACAGGAAAGAGATCGTGGGAAGCAGAACAGGTGATGGGTTTTCTGCAAGCACGAGAATGGGGTTTAATGATTCTAGATGAGGTACATACCATTCCTGCTAAACAGTTCAGAAGAGTCCTAACAGTTGTTCAAGCTCACTGCAAACTTGGTCTCACGGCAACTTTAGTCAGAGAAGACGATAAGATTCAGGACTTGAATTTCTTGATCGGACCAAAGCTGTACGAAGCAAACTGGATGGAGCTACAGAATAATGGGTTTATTGCTAGAGTCCAATGTGCTGAGGTGTGGTGTCCAATGACGCCAGAGTTTTACAGTGAATACTTGGCCATTAGAACTAGAAAACGAAAGcTGCTTTATGTTATGAACCCAAATAAATTTCGAAGCTGTGAATTCCTCATTCGTTACCACGAACGACGTAACGACAAGGTGATAGTGTTTTCAGATAACGTGTTTGCCCTGAAGAACTACGCTGTAAAGCTCTGCAAACCTTTTATTTATGGACCCACCTCACAGGCCGAAAGAATCAACATTCTACAAAACTTCCAACACAATCCTTTAGTCAATACAATATTTATATCCAAGgTCGGAGATAACTCGTTTGATCTTCCAGAAGCTAACGTCCTGATCCAGGTTTCATCTCATGGAGGATCAAGAAGACAGGAAGCTCAAAGACTTGGGCGTATTTTGCGAGCTAAAAAAGATATGGCTGCCGAAGAATACAACGCTTTCTTTTATACATTAGTATCAACGGATACCGAAGAAATGTATTATTCAAGCAAACGTCAAAGGTTTCTGGTCAACCAGGGATACAGTTTCAAGGTGATTACCAGTCTGGCTGGTATGGAGGAGGAAAATCTTAACCTTTCTACGAAACGAGAACAGCAAGAATTACTGCAAAAGGTGTTAGCGGCCAGTGATGCAGATGCTGAGGAAGAAAGGACTGCTGGGGAATCAAAtcaaaagTCTGGAGTATTTCGTCGTGCTGGTTCGATGGCGTCCATGTCTGGTGCTGATGACATGATGTATCTCGAGTACCGATCATCTTCTAAATCATCCAATCTTGCTAGGCACCCGTTGTTCAAGAGATTTAGAAAATAGACTTATATAACGTAGAACTGGAACCAAATTGGTTCAACAAGAATCACAGCCTGAATACAACCCGTTTTCTTCAGCGGGAAACCTGTCTGCATAATGATGTTACAGGCTTCTTAtacagaaagaaaataatataaaaatgcaGTTAATCTATATTAATTATACTTCTGTTTCCAGCTGatttgatcgccttccccgaaaggaattatgggtcactatttttggttagcatttttcgagcatttttcgagtatacaatgtagactcttcttgttgattgaattaaaattccaccatgagttcgactagcgtttacgattaatttaaataaggaagaactcgtatttcttaacttctcttggcagaataatgggaaatgctaatcaataTGCGATGTCGAATcttcaattctgattggttgaccttgagtttgttctgacgGTTGACTCAGCTGGTGCTTTTATCGAAACTAATCTTGAATTGgctttgggttacctgtggtttgGATGATTTGTGTTTCGCACTCCTAAGATCGGATGTAAAGCACTCCCAGGCGTTCCTTGTCATAGCGTTCAGTTAAGAGATCCTCTCACTGAGTCAGTGCTGAACGATCAACGCAGCATAAAAATCCGTTCTCTTTCCGGAACGAAACTCATTCCGGTATGATGTAAAGGGCCCGTGAGGTGAAAGGATATATTGCCAAGTATCTCTTACAGTGTTTTTTGGATTGCGTTGGTAGATTCG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q1RMT1	General transcription and DNA repair factor IIH helicase/translocase subunit XPB OS=Bos taurus OX=9913 GN=ERCC3 PE=2 SV=1
P49135	General transcription and DNA repair factor IIH helicase/translocase subunit XPB OS=Mus musculus OX=10090 GN=Ercc3 PE=2 SV=1
Q4G005	General transcription and DNA repair factor IIH helicase/translocase subunit XPB OS=Rattus norvegicus OX=10116 GN=Ercc3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003957 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16203 all species →	ERCC3_RAD25_C	ERCC3/RAD25/XPB C-terminal helicase	Domain	Interproscan
PF04851 all species →	ResIII	Type III restriction enzyme, res subunit	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001161 all species →	Family	Helicase XPB/Ssl2	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR050615 all species →	Family	ATP-dependent DNA Helicase	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR032438 all species →	Domain	ERCC3/RAD25/XPB helicase, C-terminal domain	Interproscan
IPR006935 all species →	Domain	Helicase/UvrB, N-terminal	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11274 all species →	RAD25/XP-B DNA REPAIR HELICASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003678 all species →	Molecular Function	DNA helicase activity	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0006367 all species →	Biological Process	transcription initiation at RNA polymerase II promoter	Interproscan
GO:0000112 all species →	Cellular Component	nucleotide-excision repair factor 3 complex	Interproscan
GO:0005675 all species →	Cellular Component	transcription factor TFIIH holo complex	Interproscan
GO:0043138 all species →	Molecular Function	3'-5' DNA helicase activity	Interproscan
GO:0097550 all species →	Cellular Component	transcription preinitiation complex	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase activity	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
K10843	ERCC3, XPB; DNA excision repair protein ERCC-3	EC:5.6.2.4	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 Anthopleura xanthogrammica 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 Anthopleura xanthogrammica, 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 →