Gene detail

Detailed information of XP_065065546.1 in Rhopilema esculentum

Genomic Location: ScUbCFx_10:11766645...11789035
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

LOC135691583

ATGGCTAACGACCAAGAAGAAGAATATTATGGTTATTATTACAATGAGGAAGAGGATAAAGGACTCCTAGATCCGGCTTGGGAGCGTCAGCAAACTAAGACTTTCACAGCTTGGTGCAACTCACATCTTCGTAAAGTCAACGTTCAGATCGAAGCAATTAACGAAGATTTTCGTGATGGGCTTAAACTTATGCTTTTATTGGAAGTCATTTCAGGGGAGAAGTTCCCACAGCGCCCAGAAAGAGGGAAACTACGATTTCATCAAATATCCAACGTGAATAAGGCGCTGGATTTTATCAGCAAGAAAGGTGTGAGGCTCGTTGGGGTGGGGGCTGAAGAAATTGTAGATGGAAATTTGAAAATGACTCTTGGTATGATCTGGACAATTATTCTGCGATTTGCCATCCAAGATATTTCTGTTGAGCAATTTTCATCTAAGGAAGGTCTTTTGTTGTGGTGTCAGAGGAAAACTGCTCCTTACAAGAATGTCAATGTACAAAACTTCCATATGAGTTTCAAAGATGGTCTTGCGTTCTGTGCTTTGATTCATAGACACAGACCTGATCTGATTGATTATGACAGCTTGTCAAAGGACAACCCTGCTGGCAATCTCAATTATGCATTCGAAGTTGCGGAGCAGCACTTGGACATCCCCAAAATGTTGGATGCAGAAGATATGGTTGCCAATGTTAAGCCGGACGAGAGAGCTGTGATGACATATGTTTCATGTTACTATCATGCCTTTTCAAGTTCTCAAGCGGCTGAAACTGCAGCCAAACGTATTGTGAAGGTGTTGAACGTAAACCAAGGCAATGAACAGGCAATGAACGAGTACGAAAATTTGGCATCTGATCTCCTTGATTGGATTAACCAAGTGATGCCTTGGTTGAACAACAGAAATCTTGATGACAACACACTTAAAGGTGCCCAGGACAAGCTTGAAGAGTTCCGGAACTACAACTGGAACGACAAACCACCGAAGGTCCTTGAAAAGGCCCAGCTAGAAACAATATTCAACACTCTGCAGACAAAACTGAGGCTAAGTAACCGACCAGCCTATCTTCCATCCGAGGGCAAAATGATAAATGACATCAATGGTGCATGGAAAGGCCTTGAAGATGCAGAGAAGGCATTCCAAGAGTGGATTCTCACAGAAATGAGACGTCTGGAAAGGCTGGATCACCTTGCCTTGAAATTCAAGCATAAATGTGACATTCACGAGAACTGGACATCCGGCAAAGATGAGATGCTGATGAAAGAGGATTATGCTGATCAAGGGCTTGCCTCTCTGCTCGCCATGAGAAAGAAACATGAAGCCTTTGAAAGTGATCTTGCCGCTCAGCAGGACAGAGTGGAGCAGATTGTTGCCATTGCCCAGGAGCTCAATTCCCTGGAGTATAGCAAGGTGGATGAAGTTAACGTTCGCTGTCAGAAAATATGCGACGACTGGGATAACCTTGGCCAACTGACTGGAGGGAGACGACAAAAAATTGAGGAAGCCATCGTTGTTCAAGAGAGGCTAGATAATTTGTGGCTTGAATTTGCAAAGAGAGCAGCGCCTTTCAACAACTGGATGGCCGGCGCGAAGGAGGATTTGATGGACATGTTTAGAGTGCACAAGCTTGAAGAAATCCAGGACTTGAAAGATGCCCAGGAGAAATTCAAGGACAACATGCCGGCCGCCCAGGAGGAATTCAATTCAATTATGGCTCTTGGGCAACAGGTTCAAGATCTCGGAAAAGGAATTGAAAACCCATACACTATCATAACTCTCGAGGACCTGAGCACAAGATGGGCAGAAGTTGTCGAATTGGTACCAAAGAGGGACCAAATGTTAAATGATGAAATCAGTAGACAACAGAATAATGAAAAAATTCGCTTGCAGTTCGCAGACCAAGCTAATAAGGTTGGAGCCTGGATAGAACAGAAATCCAGTAACCTTATTGAAATCAGTCTTGCGGCCCAAGGAACACTAGAGACTCAACGTAATATGATGAAGGATGTGGAAACTGATATTGCCAACTATAAGCCAAATATGGATGGCCTAGAGCATACTAACCAGCTTGCACAAGAGGCCATGATCTTTGAGAACCCACATACACCCTATTCAATGGAGGCTTTGAGAATTAGATGGGAACAGCTCATCACCTCCATCGCAAGAAACATAAATGAAATCGAGAACCAGATCCTAATGCGTGATTCCAAAGGTATCACTGAAGAGCAACTTAAAGAATACAAGCAATCTTTCAACCATTTCGACAAGGATAAAAGTGGCTTGCTTGAACCGAATGAGTTTAGACAATGTCTTGTCAGTTTGGGATATAATGTTGGCATCGATGAATCGGACGATGCCGATTTCCAACGCATCATGATGCTTGTCGATCCAAACGACACGAAAAGGGTGACATTCCAAGCATTCTTGGACTTCATGACCAGAGAACAAGCAGATTCGGACACAGCTGAGCAAGTTATGGAATCTTTCAGAATTTTAGCTGGAGATAAGGCATTCATAACAGCTGATGAACTTCGCCGTGAGCTGCCACCCGACCAGGCAGAGTATTGCATCTCCAAAATGACGCCATATGCAGGTCCCGACGCTGCTCCTGGCGCTTTGGATTACCGCTCCTTCTCAAGCGCGTTATATGGAGAAAGCGACTTGTAA

Transcript

rna-XM_065209474.1

GGGTGGGAGTTCCATCGATGCCTCTGCTATCACATCTTTCCGCATAATTCAGAAGCAAGCACAGTATTTGCCTTCCGTTCTTGCTCGTCGTTGTTCTTTTAATTTGCCTAACAAGATGGCTAACGACCAAGAAGAAGAATATTATGGTTATTATTACAATGAGGAAGAGGATAAAGGACTCCTAGATCCGGCTTGGGAGCGTCAGCAAACTAAGacTTTCACAGCTTGGTGCAACTCACATCTTCGTAAAGTCAACGTTCAGATCGAAGCAATTAACGAAGATTTTCGTGATGGGCTTAAACTTATGCTTTTATTGGAAGTCATTTCAGGGGAGAAGTTCCCACAGCGCCCAGAAAGAGGGAAACTAcgatttcatcaaatatcCAACGTGAATAAGGCGCTGGATTTTATCAGCAAGAAAGGTGTGAGGCTCGTTGGGGTGGGGGCTGAAGAAATTGTAgatggaaatttgaaaatgactcTTGGTATGATCTGGACAATTATTCTGCGATTTGCCATCCAAGATATTTCTGTTGAGCAATTTTCATCTAAGGAAGGTCTTTTGTTGTGGTGTCAGAGGAAAACTGCTCCTTACAAGAATGTCAATGTACAAAACTTCCATATGAGTTTCAAAGATGGTCTTGCGTTCTGTGCTTTGATTCATAGACACAGACCTGATCTGATTGATTATGACAGCTTGTCAAAGGACAACCCTGCTGGCAATCTCAATTATGCATTCGAAGTTGCGGAGCAGCACTTGGACATCCCCAAAATGTTGGATGCAGAAGatatgGTTGCCAATGTTAAGCCGGACGAGAGAGCTGTGATGACATATGTTTCATGTTACTATCATGCCTTTTCAAGTTCTCAAGCGGCTGAAACTGCAGCCAAACGTATTGTGAAGGTGTTGAACGTAAACCAAGGCAATGAACAGGCAATGAACGAGTACGAAAATTTGGCATCTGATCTCCTTGATTGGATTAACCAAGTGATGCCTTGGTTGAACAACAGAAATCTTGATGACAACACACTTAAAGGTGCCCAGGACAAGCTTGAAGAGTTCCGGAACTACAACTGGAACGACAAACCACCGAAGGTCCTTGAAAAGGCCCAGCTAGAAACAATATTCAACACTCTGCAGACAAAACTGAGGCTAAGTAACCGACCAGCCTATCTTCCATCCGAGGGCAAAATGATAAATGACATCAATGGTGCATGGAAAGGCCTTGAAGATGCAGAGAAGGCATTCCAAGAGTGGATTCTCACAGAAATGAGACGTCTGGAAAGGCTGGATCACCTTGCCTTGAAATTCAAGCATAAATGTGACATTCACGAGAACTGGACATCCGGCAAAGATGAGATGCTGATGAAAGAGGATTATGCTGATCAAGGGCTTGCCTCTCTGCTCGCCATGAGAAAGAAACATGAAGCCTTTGAAAGTGATCTTGCCGCTCAGCAGGACAGAGTGGAGCAGATTGTTGCCATTGCCCAGGAGCTCAATTCCCTGGAGTATAGCAAGGTGGATGAAGTTAACGTTCGCTGTCAGaaaatatgCGACGACTGGGATAACCTTGGCCAACTGACTGGAGGGAGACGACAAAAAATTGAGGAAGCCATCGTTGTTCAAGAGAGGCTAGATAATTTGTGGCTTGAATTTGCAAAGAGAGCAGCGCCTTTCAACAACTGGATGGCCGGCGCGAAGGAGGATTTGATGGACATGTTTAGAGTGCACAAGCTTGAAGAAATCCAGGACTTGAAAGATGCCCAGGAGAAATTCAAGGACAACATGCCGGCCGCCCAGGAggaattcaattcaattatggCTCTTGGGCAACAGGTTCAAGATCTCGGAAAAGGAATTGAAAACCCATACACTATCATAACTCTCGAGGACCTGAGCACAAGATGGGCAGAAGTTGTCGAATTGGTACCAAAGAGGGACCAAATGTTAAATGATGAAATCAGTAGACAACAGAataatgaaaaaattcgCTTGCAGTTCGCAGACCAAGCTAATAAGGTTGGAGCCTGGATAGAACAGAAATCCAGTAACCTTATTGAAATCAGTCTTGCGGCCCAAGGAACACTAGAGACTCAACGTAATATGATGAAGGATGTGGAAACTGATATTGCCAACTATAAGCCAAATATGGATGGCCTAGAGCATACTAACCAGCTTGCACAAGAGGCCATGATCTTTGAGAACCCACATACACCCTATTCAATGGAGGCTTTGAGAATTAGATGGGAACAGCTCATCACCTCCATCGCAAGAAACATAAATGAAATCGAGAACCAGATCCTAATGCGTGATTCCAAAGGTATCACTGAAGAGCAACTTAAAGAATACAAGCAATCTTTCAACCATTTCGACAAGGATAAAAGTGGCTTGCTTGAACCGAATGAGTTTAGACAATGTCTTGTCAGTTTGGGATATAATGTTGGCATCGATGAATCGGACGATGCCGATTTCCAACGCATCATGATGCTTGTCGATCCAAACGACACGAAAAGGGTGACATTCCAAGCATTCTTGGACTTCATGACCAGAGAACAAGCAGATTCGGACACAGCTGAGCAAGTTATGGAATCTTTCAGAATTTTAGCTGGAGATAAGGCATTCATAACAGCTGATGAACTTCGCCGTGAGCTGCCACCCGACCAGGCAGAGTATTGCATCTCCAAAATGACGCCATATGCAGGTCCCGACGCTGCTCCTGGCGCTTTGGATTACCGCTCCTTCTCAAGCGCGTTATATGGAGAAAGCGACTTGTAACCAACCAAAGAACTAcgcattgaaaattgaaatgacaTGCTTCCAGTATTTTTGTAACAAGAGAAGGAATCTAGAGACTCGCTTTGGTGTAGTTCTGAGCTGAAGATCTCTCGTTACTATTTGTCTAGGACTAACAGCTTGTCTTCAGAAAATATGGGAAATTTATTCTAATCATGAATTGTCAAATCAGCTGATTTTTGGGTTTTTTCAATTAGGATTAATGGAATCTTGTGATTTTGGAGAACGAAAA

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002499 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00435 all species →	Spectrin	Spectrin repeat	Domain	Interproscan
PF13405 all species →	EF-hand_6	EF-hand domain	Domain	Interproscan
PF00307 all species →	CH	Calponin homology (CH) domain	Domain	Interproscan
PF08726 all species →	EFhand_Ca_insen	Ca2+ insensitive EF hand	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001589 all species →	Conserved_site	Actinin-type actin-binding domain, conserved site	Interproscan
IPR002017 all species →	Repeat	Spectrin repeat	Interproscan
IPR011992 all species →	Homologous_superfamily	EF-hand domain pair	Interproscan
IPR018247 all species →	Binding_site	EF-Hand 1, calcium-binding site	Interproscan
IPR002048 all species →	Domain	EF-hand domain	Interproscan
IPR001715 all species →	Domain	Calponin homology domain	Interproscan
IPR036872 all species →	Homologous_superfamily	CH domain superfamily	Interproscan
IPR018159 all species →	Repeat	Spectrin/alpha-actinin	Interproscan
IPR014837 all species →	Domain	EF-hand, Ca insensitive	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11915 all species →	SPECTRIN/FILAMIN RELATED CYTOSKELETAL PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0030036 all species →	Biological Process	actin cytoskeleton organization	Interproscan
GO:0030054 all species →	Cellular Component	cell junction	Interproscan
GO:0030864 all species →	Cellular Component	cortical actin cytoskeleton	Interproscan
GO:0042995 all species →	Cellular Component	cell projection	Interproscan
GO:0051015 all species →	Molecular Function	actin filament 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
K05699	ACTN1_4; actinin alpha 1/4	-	Exosome	ko04147	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 →