Gene detail

Detailed information of XP_065058613.1 in Rhopilema esculentum

Genomic Location: ScUbCFx_10:10171798...10218396
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_065202541.1

CCTCACTTCTAGATGCCGCGAAAATGGTTATGGCCTAGTGCTCTCTCAAAGGTCCAGTAAGTATAAAACGTGGTCTTCGTTAATTTGCGTTATCTTATTTGGATCTGTAATCTATTTGAACGGAAAGAAGAAGCTGCCGAAATCATTATGGAAGTAGCAACACATTTTCGGCTAGAAGCCTTCTGACACAAACACCTGGAATATATATTAGGGAAATCTAATGGACTCAATCAACAAAGGGTGGATTCTAATTCCACAGAACCTGGAAAAAACTCTTCTGAAAGGAATTCTTTTTGCCAAGAGTCAGGAATTTGAAATAGAAGTAAAGTTGAGCACAGTATCAGACATCAAGGATGCtagCTTCAACTGTGACTGGGAGTTGAAAAACTTGTTGAATGGATTTGAAGATTCACTTAAGCAGAGTTTGCACAATTCCAAAGATCTTGATGAATTCATGCATGAGGTCCACAGTTTAACAAGTAAGTTAGTCAAAATCCGGGATCGAAGGTCGCAGCGGCACTTCTCAACATCAGAACCAGGTCATTTTTCCACAGTCATAAAGGAAATTGAAGAGTTAGGTTGGGAAAAATTATTGCATCTTGACGCCAGCTTCAGTTCAATGACACTGATAGCTAAAGACGTTGCTTCGAGAGAGCACCTTTTGAATGTACAGTATCACACCCAGGATGGTGCAAGAACACTGCTTTGCCAAACTGACCTCCCAGCTCCTTTTCGTCCCATCATAAAAGCAAAGGATGGCGGTATCTGTTATGTACACCAACAGTTCGTTCAGGAACTGGAGAAACACCAAGATTTTTGGGACATAATTGGAGAATTTGACGAGAATTGCTGGGTGCTTGAGCCAGAGACCCAGTCGTGGTCGTGCTGTTTTCGCAGAGTCGCCCTTGGGAGCAAAGCTTCGTTACTGGTTACGATTGCCCCTTCGCAGCCAAGATCGTTGCCGGTGTGTCGGTTTTTAGGTCCAGATCAAGTCGTTGGTCCTCTTCGTAGCAAATGGAACCACGATATCGCTCTATGGGATGTTGAAAAAACAGTCCTTTGCAACATCAAGGATATTCTAGAGATAGATTTACCAGCTCCACTGGATAAAAAAACGGAGGATTTCAGCATGCACTGCAGTATTTGCTACGCGTATCGACTGAATGACGAAGTACCAGAAGTGGCATGCGATGATTCCCGCTGTGGACAGCTGTTCCATTCCGCGTGTCTCATCGAGTGGTTCCGTTCCTTGCCAAACTTTCGACAAAGTTTCAATGTTATGTTTGGTGAATGCCCTTACTGTTCTACGccAATGACAGTAAAGATGTCAAAGAAATCGAAATAATTGAAGAGGCACCACGTATTGGATAACTGTTTTAGTTTATAGAAAACCATATTTTCTACGCAAACATCAGGTATCTTTAcgaatttcaaaacagtttgttagtattttgaatggaaaagaaaagcattgcatttttaatttaaaacccagaaaaaacagaaaatttgtttggccAAACTTTCTGAATTTTTGCAGTTACGGACTCTTTCCAGTTGGGACATGAAAAGAAAGCCCGAGTAAATGCGCTCAGAAGTTTCATGACGAAATCTTTCCGCTCTTCAGGGAACCCATGCTCAACAACAGAAAACTTAACTACTTCTATCTGCCAAGAACGAAAAAAAGGGTGGAAGAAATAAGTGAAGGGAGTTTTAGAAGCTCAAGAACTAAACCCTTTTCTTCCTGTGCGTGAGATGTATTTCCAAGAGActttacagcaaaaaattcagttttgcAATACTCCAAATGATCAATTCTTCAAGCCTCTAGGCTTAAATTTCTTACCACAAGAAGGTcggatgaaaacatcatttttattcctttctGCCATCACCATAACAGCTTTCCAGTTGCTGTTGCATATTTCTGACCATCGACGGTTAAAGAGAAGTtattattgacaaaaaaaatattacaaatttcatcaattttccAAGCCTTACAAAGGTACCCgatttttaatgaataattttttcatccaaaacttgcctcaaacaattctaaaaaaagcaTGAATACGTTTGAATCAGCTCTCGACTCTATAAACAGTttttctgctctaaaaatgcagtgTTCTTGATAAGGATATTCGTTAAAAAAGGCAACGatatagccttaccaaaatacgcggtatttcacaaaaaaaatatttttatccaaaactttcCTCAATACACTCTAAATGAGGCATAAAAACGTTTTAATCTTATCTTGACTCTATCGAAGgagtttttttctttaaaaatgcagTGTTTTCGATAAGGATTTCAGTAAAAAGGCAAGGCCTTACAAAAATACGcgatttttaacaaaaaatttt

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005658 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11793 all species →	FANCL_C	FANCL C-terminal domain	Domain	Interproscan
PF18890 all species →	FANCL_d2	FANCL UBC-like domain 2	Domain	Interproscan
PF18891 all species →	FANCL_d3	FANCL UBC-like domain 3	Domain	Interproscan
PF09765 all species →	FANCL_d1	FANCL UBC-like domain 1	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR026850 all species →	Domain	FANCL C-terminal domain	Interproscan
IPR026848 all species →	Family	E3 ubiquitin-protein ligase FANCL	Interproscan
IPR043898 all species →	Domain	FANCL, UBC-like domain 2	Interproscan
IPR016135 all species →	Homologous_superfamily	Ubiquitin-conjugating enzyme/RWD-like	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR044037 all species →	Domain	FANCL, UBC-like domain 3	Interproscan
IPR043003 all species →	Homologous_superfamily	FANCL, UBC-like domain 3 superfamily	Interproscan
IPR019162 all species →	Domain	Fanconi anemia complex, subunit FancL, WD-repeat containing domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13206 all species →	UBIQUITIN LIGASE PROTEIN PHF9 FANCONI ANEMIA GROUP L PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006513 all species →	Biological Process	protein monoubiquitination	Interproscan
GO:0036297 all species →	Biological Process	interstrand cross-link repair	Interproscan
GO:0043240 all species →	Cellular Component	Fanconi anaemia nuclear complex	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase 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
K10606	FANCL, PHF9; E3 ubiquitin-protein ligase FANCL	EC:2.3.2.27	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 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 →