Gene detail

Detailed information of XP_065064217.1 in Rhopilema esculentum

Genomic Location: ScUbCFx_4:5752299...5760877
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

LOC135690556

ATGGTGCAAGGCCCGCGGAGCATATTACAGATTGAGGGGACTAAAACGTTTTGGGGGGCTAAACATGGTAAAAATCAAAAGCAGGTTGAATTTTTGAGAATAATTGGGGAGGGGGCTAAAGAAAGTTCGGATAGATGTTACTCTAGATTTAGAGATGAGAAATCTAGCGAGTTGTTGGTGTTTCGCGAAATGACGGCTAGAGTGAGATTGAGGCTGAAAAACAGGCGGGAAATGATCCCCTGTGTTTTGAAAATGTCTGATCCCATCGAATGCCCGGTTTGTAACGGTAAATTTTCAGCATCAGTGATAAATGATCATGTGGAGGCATGTTTAGACAAAGAAGATTGTTGTTCTGCAAAAAGCTGCAATAAAACAGTTTCTTCAGTTAACAGAGAGGTAGACCTGGAAAAGGAAGATCAGAAAGTCATTCCTTCGCCATCCGCTAAAAGTCTTTCAGGTTGCGAAGTCGGGACACTTGCAGGAAACGATACTCTTTGTAAATCGGTGCATGTGAATGAAAACATGGAAGCTGTTCCAAAGTTGAAATCAACAAAAGCAAAGGAGGAAAAATGCAAGCCCATTAATGCCCATCGATCAATTTTTGACATATTAGGAAAACGGAAGTACTCCGCCCTATCAAAACAACCAATGAATGAAGAAGACAGAAAACGAATCAGATTTCCAGGAAAAAATAGTGAATCCGCGCGTGAAAAGCAGTTTTCTTTGCAGAACAGTAATGGGGAGGCTTTAGTCAAGACTAATGGTTTGGATGAAAGGGAGGTGAAAGGTTTTTCTCCATCAGCGAAAACTAATTCAAAGGCTATCGATCTTGAAAAACCTGTACCATTGGCTGAACAAATGAGACCTATAAGTTTTGATGATTATGTTGGTCAAGACGAACTAATCGGGGAAAATTCTACCCTTAGAGCTCTTTTATCATCTGAAAAAGTTCCTTCTTTTATTCTTTGGGGTCCACCTGGTTGTGGAAAGACAAGTCTTGTAAATATCATTGGAAGCAGATCAAAAACCAACCCCTTGAAGAGATTGGTAAAACTCTCTGCCACCGCATCAAGTCTGAGTGATGTAAAAGAAGCTATTAAAATTGCCAAAAATGAATATTCCATGTTCAAGAAAGAAACAATTCTTTTTATTGATGAGATCCATCGATTCAACAAACTTCAACAGGACTTTTTCCTACCTTTTGTGGAGAATGGGACAATAACTCTTATAGGAGCCACAACAGAAAATCCCTCATTTCAAGTAAACGGTGCTCTACTAAGCAGATGCAAAGTTATTGTGCTAAAGAAACATAGTGTTCAGAGCTTGATGAAGATACTCAGACGTGCAGTGGAAGGGATCGGGGGGAACATTGTACAAGAGATTCCAGAGAAATGTTCAAGTGAAGCCTCAAGACTGTTCATCTTGGAAAACGCATTAGAAGCCCTTGCAAATCTTTCTGACGGGGATGCTAGAAGTGCATTGAATGGACTTGAAATGACAATTAATATGAAAAAGTCCCATAATGACAACAACTGCATACAAGTTTCTGATGTCTCTTCGATACTGCAAAGAAACCATATTCTATACGACAAAAAGGGGGAGCAGCATTTCAACCTGATATCAGCCTTTCATAAATCAATAAGAGGCTCTGATGACAGTGCTGCCCTGTATTGGTTATCGCGAATGCTGATTGGTGGAGAGGATCCGTTGTATATTGCAAGAAGAATGATACGAATAGCGAGTGAAGATATTGGAATAGCAGACAATTCAGCTCTGTCAAAAGCTGTTTCAACGCACCAGGCGTGCCATTTTATTGGAATGCCAGAATGCGAGGTCAATCTTGCTCACATGGCTGTATATCTGGCTCGTGCACCGAAATCAGTCGAAATCTACAAAGCGTACAATGCTGCAAAGAATAGTGTGCTCACATGGAAAGGACCCTTGCCAGGTGTACCATTGCACCTGCGTAATGCGCCGACGAAACTAATGAAGGAATTGGGATATGCCAAAGGCTACAAGTATAACCCGGACTATTCTGGATATGTTGAGCAGGAGTATCTTCCTTCAGAATTACAGGGAACAAACTTTTTTGAAACTGGATGCTCGTAG

Transcript

rna-XM_065208145.1

CATCAAAGTATGTCCAAAGGTACCATGGGGATGCTTCTCTAAAATGTgtgacaaagaaaattgtacGGAAAAGACGCTGATAAATGGTTTTACCTCTCCCCGTGTTTTAAAGGCGTCAGTTCAAGATATTCCGCTGTCAGATAGCAACGACCAATTTCTTAACTTAAAGAAAATCGTTTTACATAGGCCGCGGCGGTTGTGATTGAACATTTTCCGTAGCCTAGCTCCTGGTTTTGGAAAATGCTCGTACTTGGTAAACGCAGCAGGTATTAAACGATtaccaacattttctcattacCAGAGAGCAAGAGTTGCTAAATACCATGGTGCAAGGCCCGCggagcatattacagattgagggGACTAAAACGTTttggggggctaaacatggtaaaaatcaaaagcaggttgaatttttgagaataattGGGGAGGGGGCTAAAGAAAGTTCGGATAGATGTTACTCTAGATTTAGAGATGAGAAATCTAGCGAGTTGTTGGTGTTTCGCGAAATGACGGCTAGAGTGAGATTGAGGCTGAAAAACAGGCGGGAAATGATCCCctgtgttttgaaaatgtctgaTCCCATCGAATGCCCGGTTTGTAACGGTAAATTTTCAGCATCAGTGATAAATGATCATGTGGAGGCATGTTTAGACAAAGAAGATTGTTGTTCTGCAAAAAGCTGCAATAAAACAGTTTCTTCAGTTAACAGAGAGGTAGACCTGGAAAAGGAAGATCAGAAAGTCATTCCTTCGCCATCCGCTAAAAGTCTTTCAGGTTGCGAAGTCGGGACACTTGCAGGAAACGATACTCTTTGTAAATCGGTGCATGTGAATGAAAACATGGAAGCTGTTCCAAAGTTGAAATCAACAAAAGCAAAGGAGGAAAAATGCAAGCCCATTAATGCCCATcgatcaatttttgacatattaGGAAAACGGAAGTACTCCGCCCTATCAAAACAACCAATGAATGAAGAAGACAGAAAACGAATCAGATTTCCAGGAAAAAATAGTGAATCCGCGCGTGAAAAGCAGTTTTCTTTGCAGAACAGTAATGGGGAGGCTTTAGTCAAGACTAATGGTTTGGATGAAAGGGAGGTGAAAGGTTTTTCTCCATCAGCGAAAACTAATTCAAAGGCTATCGATCTTGAAAAACCTGTACCATTGGCTGAACAAATGAGACCTATAAGTTTTGATGATTATGTTGGTCAAGACGAACTAATCGGGGAAAATTCTACCCTTAGAGCTCTTTTATCATCTGAAAAAGTtccttcttttattctttggGGTCCACCTGGTTGTGGAAAGACAAGTCTTGTAAATATCATTGGAAGCAGATCAAAAACCAACCCCTTGAAGAGATTGGTAAAACTCTCTGCCACCGCATCAAGTCTGAGTGATGTAAAAGAAGCTAttaaaattgccaaaaatgaatattccatgttcaagaaagaaacaattctttttattGATGAGATCCATCGATTCAACAAACTTCAACAGgaCTTTTTCCTACCTTTTGTGGAGAATGGGACAATAACTCTTATAGGAGCCACAACAGAAAATCCCTCATTTCAAGTAAACGGTGCTCTACTAAGCAGATGCAAAGTTATTGTGCTAAAGAAACATAGTGTTCAGAGCTTGATGAAGATACTCAGACGTGCAGTGGAAGGGATCGGGGGGAACATTGTACAAGAGATTCCAGAGAAATGTTCAAGtGAAGCCTCAAGACTGTTCATCTTGGAAAACGCATTAGAAGCCCTTGCAAATCTTTCTGACGGGGATGCTAGAAGTGCATTGAATGGACTTGAAATGACAATTAATATGAAAAAGTCCCATAATGACAACAACTGCATACAAGTTTCTGATGTCTCTTCGATACTGCAAAGAAACCATATTCTATACGACAAAAAGGGGGAGCAGCATTTCAACCTGATATCAGCCTTTCATAAATCAATAAGAGGCTCTGATGACAGTGCTGCCCTGTATTGGTTATCGCGAATGCTGATTGGTGGAGAGGATCCGTTGTATATTGCAAGAAGAATGATACGAATAGCGAGTGAAGATATTGGAATAGCAGACAATTCAGCTCTGTCAAAAGCTGTTTCAACGCACCAGGCGTGCCATTTTATTGGAATGCCAGAATGCGAGGTCAATCTTGCTCACATGGCTGTATATCTGGCTCGTGCACCGAAATCAGTCGAAATCTACAAAGCGTACAATGCTGCAAAGAATAGTGTGCTCACATGGAAAGGACCCTTGCCAGGTGTACCATTGCACCTGCGTAATGCGCCGACGAAACTAATGAAGGAATTGGGATATGCCAAAGGCTACAAGTATAACCCGGACTATTCTGGATATGTTGAGCAGGAGTATCTTCCTTCAGAATTACAGGgaacaaacttttttgaaactgGATGCTCGTAGGATGTAAAATAGGGCCGTTCAAAATTGATGAGAAGATATctaatggaaaaatatattacatCAGATCGGAAATATTACAACATATATTCTTTCATGCTATAAATTTTAAGTGATTTGCTGTATATGGCGAGGCTTTTCTTTGTTAACTCCGTCAAAGGTTACCCCGGGAAACCCTTTTAAGTCAGTCGAAAATCCATTAAAGTGCCACTGAACTACTTTCGTGAGAATTTTGACAATGTGTGTTTTCTAATGAGAATGATCAAATAAAAGCTGCTGAATCGAA

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005454 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12002 all species →	MgsA_C	MgsA AAA+ ATPase C terminal	Domain	Interproscan
PF16193 all species →	AAA_assoc_2	AAA C-terminal domain	Family	Interproscan
PF00004 all species →	AAA	ATPase family associated with various cellular activities (AAA)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR021886 all species →	Domain	MgsA AAA+ ATPase C-terminal	Interproscan
IPR032423 all species →	Domain	AAA C-terminal domain	Interproscan
IPR051314 all species →	Family	AAA ATPase RarA/MGS1/WRNIP1	Interproscan
IPR008921 all species →	Homologous_superfamily	DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal	Interproscan
IPR003959 all species →	Domain	ATPase, AAA-type, core	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13779 all species →	WERNER HELICASE-INTERACTING PROTEIN 1 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0000731 all species →	Biological Process	DNA synthesis involved in DNA repair	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006261 all species →	Biological Process	DNA-templated DNA replication	Interproscan
GO:0008047 all species →	Molecular Function	enzyme activator activity	Interproscan
GO:0017116 all species →	Molecular Function	single-stranded DNA helicase activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	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
K07478	ycaJ; putative ATPase	-	Replication and repair	-	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 →