Gene detail

Detailed information of XP_065059485.1 in Rhopilema esculentum

Genomic Location: ScUbCFx_217:9170569...9197209
NR annotation: no NCBI-NR hit recorded
Species Rhopilema esculentum · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_065203413.1

AATGCGGAGGAGTATTCGTATGAAAAACGTATGTGAATGGTCAGAAGGCAGACAACATTCGAAGGTTTTGATCAGGAAGAGGTGTTAGGGGAAGAAATGGAGAACAGTTTAGTCCCAAATGAAACTTATAGCTTATCGAcgaaagaagaaacaaatcagagcaaagaattattttttgttaagttaACTGACTCATCACTTCGTGCCGTCGAAGAGTACTTGGAGAATAAGGCAGCCATAAAAGGGCATCCAAAAATCCAATTCTTCGGGCCGAACGGACTTCTTCACCTTCCAAGTCGTCCTGGATCTGCAAGTCAAGATGttggtaaaaatttcaaattttcctgctcattttttgcaaGGGATGGGAGGCAGGGAATCACAGAATGTTTGCATCAGCCaagcaaacataaaaaaatgttggGCTCAATGGGTatgattgagaaaaaaattgcagttatgGGAACAGATGAGGCTTATGAAATGACTAGAAACAAAATGGCACAAGCTGATCAAGAACGAAAAGGAGTCAgGACCAaggaaatcaaaattaatcattCGAAGTCAAAAAAGAAGATCACTCCTGTCGGAAAAGAGATGaataatgcaataaaaaagaagttagcAGGAAGTTCGTCGTTGTTGAAGCCAATAAATGGTTTAAAGCCAGCGACTACCGCCGGATCATCATCAACTTCGAAGGGATCAAGTTGCAAAGATCGCGTAATTCATATTCTTGCCATTAGACCTCACAAgaagcttgaaattttttcaaggctcCAGAGAGagGGCAtaaatcaaaaagaaagaaacactCTTGGGGCAGTGCTGCAGCAGGTTGCCACCATGCAAGATAACTCCTTTAAATTAAACAAGCACTATTATAACGAAATAAAGCCTGACACATGGCCTTACTATTCGGAAGCCGAGAAAACAGCCGTTAAAGAAAGTTTAGCTCAGTTGATGAGCCAAGACTCAAGTCCGAAGGTCTCGTCAACATCGAAATCACCCGAAGAAAAAGGAATTAAAAGACAATTGAATGATGACTACAACCATTTATCgtccaaaaaacaaagaatagcAAAACCAATTCAAGATCCGTCACCCTCGTCTTCGATTGCATCAAAAGGAGACTCGAATCGTGATCATAATTCAAGTAAAAAGCGATCTGATCAACAAACTCGAACTCCAAATAATGCACATAAATTATCGGGTAAAACAGAACTTTCAAAGAACGGAATATCACGGAATGGGACAGAACGTTCCGggacaaaactaaaaaacgagccttcaaaaaatgaaatttcaagtaATGGGACGACTCCTTCTGTACAAAgattaaaaactgaaaagccTGTTGCTCGTATATCACCTATAAATTCTTACATGTATAATGGGAAGGAAGCCAGGTCGGTGGTGCAAGAGGAAGAATCGTCTCCGCCAACCGTTGCCTCGACGTCGGATATCCCTGATCATGTTCTAAAGTACCAGCCTATCAAATCGTATGAACAGAGATGTAAATACAAGCAGGATTTCCAAGCACAGTACAGAGAGTATATTgaactaaaagaaaacatagaCAGAGTTtcgaataaatttttagagtTGGATCGAATTAGGCGGAAGCACCCAGAAGACAGCCAAGCCGCCCAAGAAataaagcagaaaatattttatctctaTGAAGAACACCAAAAGGATGAAAAATAccaagaaatgaaacaaaaatacgCGGATCTCTATGCCAGACTGAGTCACATAAAAAAGCTAGTAGTTGAGTATGACCAAAAGCATTTTCAGGTGGCATCATGATGCACCCTTGAGTAGTAGAGCTTAGAGTTGAGTAGTTCATGATGCTCGTCAGGTATCGTTCGCAATTTGTGCTTGCATTTTGGATATCTGGGTACTTTTGCCTCGTCGCTTTCTTACACCTGTTTTGCAAGTCAAAGTTACTCGCCTTGTATTTCTGAATACTTCTAATACTTAATACTTGACACTTCTGGGTActtctgaaatatttgaaatgcaCGTTCTACTGTCCTTTTTGTCTTCAACAAATTTGAGTTTTAGGAAGCCCTTAAAGGATTTGTTGCTATTCTGTAATGTTTACCCCCGAATAACACTCAaatcattatttctttcaaaagttctCACGTAGCTTTTGCGCGAAATGAAGTGAATTCCTTTAATGTCGTGTTAGCCTGTTCTCTGTTCATTATTGCCCATAATTTATTGTGGGTGTAGTGTAGAGCAGTGTAGAATTTTGGTTGCCCAGTGTCAATGTTCTATCCTTGATAGAAAAGGACGTACAATTTTCGAAATACCTGTACGATGTGAATATGAGGTCTAAGTAGATAACTCAGGGGCTAGACTTAAAGTATGTTGCTTACTATTCTCGTCCTAAGTATATCgtgaatttcttttgcaaaatgatattttggaGTTGAACACCAATTATTTTGTGGATAAgctgcaaaatgttttgtggtTTTAGAATATTCTCATAAATTTTATCGGTATTTTCTCCTTAAGCCAGTCCGTATGTTATTAATCCTTGCAGCCATCGCATCCCGTGTAATGTTACGTTTCTTTCGAAGTACTGATTGTTGCTTTTTTGCCCGTTGCGTGCTACCTTTCTATAAGAAGAACCCTTTAACTCTGAgagaattgttatttttaaattctttttcaatcgAAGATGTTTGTAAGTTGATTTTGTATTGTGTGGCctaatttttcttgtatttgttTTCGTTTCATTCGCTATTTAAGGGTTTGTCGCTCACTTCCAATTAATTGCCAGTTTAAAGCTATTGCTGATCTTTCATTGCTTGTAttcaaaaagataatttatttttaaagatgaaatcTTAGGTTTTTAGGATTCTTTGGTATCAGCAATGAAGCCCTCAATTGTGATTCCCATGTCCTAAAGGGCATCCCTATAATTAGAATTTAAGTGTATATCAGAGCTAGAGGTATTCACCCCCAAACCTTAGGAGCAGGGAGAATACTGCCCCCCCCTAATGATAGGGATGTCTATTCTCCTTCCCTAATTGACactaatttgaaaaaaaaatacattctATTACATAGTATTAGAGAGTCTTCAGGGCTTTGGTTGTAAAGAAACTCTCTAGTTAATATTTACCAAAATTGTCCAGTTCATAAGCTTTAAGAGCTATAATGTTTTGGTCaggattttttaattaaattttctttaggagTATGGTCATTGTCctacaattttgaattttgacttTGTTATATTTCAAATAGGTTGTTTTTTCTTGGTCTAACTTAAATACTAAGGATGTAGGCTATTTGGTAAAAGAATTTTTCCTAATATCTTTATACCAGCTAGGGGCCACTGTTTTAGCTAAAGAAATTGAGGTGTAATCTTGTTGTAAATCTTGTATTTCTTCGCAACATTGAATCAGATAAAACCACTTTTGTACCAGAAAATGAACCTTCTTCCACTTCGTATTGTAGAATGTGAGGGGCCTGGGGATGAGTTAAATTTCGCACAGTCAAACTCTAGTACGAAGCGTTGTTGTCATCGAAGAGGGACACATTTTCCACCAACTGAGATTGAGAGAAAGCataaaaaccaattttgattggtttcAAGTGAAATCTCCTCtctttgataaagtttttcttttaccAATATAGTGAAAATAGCATTGCGATTTTTGAATCAGGAGAATATTGCATCGGACAGTTGTTCAATAGTTACAAGGAAAAAAGCTTTCTTGTTGTGTTAGTTTTATTCATTCCCTCGAGAGTTTGATTGCAGCGTGATTGCTCTTGCCCATAGCAACTTACATGTCCCGtcaatttaattcttttcacCCTCTAATCGCCtgtttcttgaattttgtattatttatGACTTTGCGTGTAGATATGATTTGATTGttcaaaacaaggaaaaactGTAGAACTTTGGGTCGttgaattcatttatttgtgTCGACATTAAAAGTGAAtaataaatattgataa

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006362 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10390 all species →	ELL	RNA polymerase II elongation factor ELL	Family	Interproscan
PF07303 all species →	Occludin_ELL	Occludin homology domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019464 all species →	Domain	RNA polymerase II elongation factor ELL, N-terminal	Interproscan
IPR042065 all species →	Homologous_superfamily	E3 ubiquitin-protein ligase ELL-like	Interproscan
IPR010844 all species →	Domain	Occludin homology domain	Interproscan
IPR031176 all species →	Family	ELL/occludin family	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23288 all species →	OCCLUDIN AND RNA POLYMERASE II ELONGATION FACTOR ELL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006368 all species →	Biological Process	transcription elongation by RNA polymerase II	Interproscan
GO:0008023 all species →	Cellular Component	transcription elongation factor complex	Interproscan
GO:0000987 all species →	Molecular Function	cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0032968 all species →	Biological Process	positive regulation of transcription elongation by RNA polymerase II	Interproscan
GO:0042795 all species →	Biological Process	snRNA transcription by RNA polymerase II	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
K15183	ELL; RNA polymerase II elongation factor ELL	-	Transcription machinery	ko03021	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 Rhopilema esculentum 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 Rhopilema esculentum, 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 →