Gene detail

Detailed information of XP_065053259.1 in Rhopilema esculentum

Genomic Location: ScUbCFx_1662:5106799...5135622
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

LOC135682336

ATGGCGCTCTGGAACAAGCTCCAAACTCTCGATGATGAGGCTCGTACAAAGCTTGGAGAAATTTATGGGAGTAATAATTTCCCTTTAGAAGTGAGAGGGATGTTTGCTGAATGGATTGAATCGCAGTCATGGAGTATATTTGATCAGAACATACCAGAACATACCCAAGAGGCAGAGAGTCTTGTGAATGAACTAATCAAAAAGTTAGGGGAAAAATCTCAACAGCAGCCTCATGACTTGATTACTCAAATGAGGTTTAAAGACCTACAGAAGCAAATAAAGGATTTATATCAAAACAACCCTTGGTCCTTAGTCCTTACCATAAAGGAAATACTGACAGCCGAACAAAACCTCCTCATTAAAGCTGAAAAGCCGATGAGCGTGCAATCGCCGATGATGGAGATAGAAACACCAGAAAGCCCATCAATTTTAGATATTGGCCGATTCATTGACGATCTCAAGTCTGCGGCGCAGAAAACTGACATGGATTTGAAAAACTATAAACAGCAACAGGAAGATTTTGTCATTCGATACCAGGAGATATGCAAAGTTGACGTGGAAATCAGCAAGGCCACAGAGCGCCGTGATACTAAAGACCAGATGATTATACTGCAAAAGAGGAAAGCTGATATTGAAAACATGTTGAAAGAAAAAGCCCTTGAAATCCTCAATGACCGTGAGGCGATTTTTATACAGCTGGAAAGTCTTAGTTTGAAGATAGAACAGGTTTCCCAAAAGGTTTACCAAGAATTGTTTTTGTGGCGTATGAATCAGCAAAAGTCACTCAGTGGAGGAGACAAGCCAGACCCACTTGACGAATTGCAAAACTGGTTTGAAGCCTTAACAGACACATTGTGGTCCATGTACCAACTGTGCACGCAGTTCAAGTTACTTTTTGATGCTCTGCCAATTATAAGGAATGGCGATGAAAGGGATAAAACCGAAAGGGTCTTAGCAGACGCAGTATCAAGCCTCACAAAGCTAATCCAGAGGTCATTTATTGTTGACAAGCAGCCACCACAGGTTCTGAAAACCCAGACAAAATTTCAAGCGTCTGTTAGATTGCTGGTTGGTACCAAGCTCAACTTGCAGCTTAACTGCCCAGAAGTTGTTACAACCATTTTAAGTGAGAAGCAAGCCAAAGAGCTATGCCATGGAAAGACGATAGAAGATACTGGTAGCTGTGGTGAAATTCTGAACAACAGAAGCGTAATGGAGTACGACCAGCAATTGAATGCGCTACATGCAGACTTTAAAAATTTGTCCTTGAAGAAAATAAAGCGTCAGGACAGAAAAGGACAAGAGTCTGTGCTAGAAGCGAAAAGCTGTTTGGTGTTCTCTGCAGCGATAACAATTGGAGGAGAAAAGCTTCCAGTTATGTGTATGTCTGTACCAGTTGTGGTTGTTGTGCATGGCAACCAAGGCCCAAATTCTGAAGCAACGATATTTTGGGACAACTTTTTTTCAAACCCGGACCGAGAACCTTTCGAGGTGCCAGAGGAAGTCGACTGGGATGAAATGTCCTTCGCTCTTAATGCAAGATGGGCAATGACGACAGAGTGTGACTTGAAAGAAGAGCATTTGGAATATCTAGGCTCGAAATTGTTTCAAAATTGTGAGAAATCCCAAAGCAGCCGTAAGAAGGTATCTTGGCATGCATTTAATAAGGAGCCATTGAAGGGTCGCAATTTTACTTTCTGGGAATGGTTTCATTCAGGAATGGAGGTGGTGAAAAGGCATCTTAAAGATCATTGGAAAGAGGGATATCTGGAGTTCATGTCAAGAGAAGAGGCTCGCAAGAAACTGAATGATATGTGTGTTGGGACGTTTATAATAAGATTCAGTGACGGAGAAGTTGGAGGGGTCAGCATTGCTTGGGTTATTGAGAAAGAAGGGGGAGGCGCTGATATATGGAATGTGCAGCCGTGGACTACGAAGGATTTCAACATCAGATCTCTTGCAGACAGGATCTTTGATTTGGATCTGTTGAAATACGTCTATCCTGGTGTTGAGAAGGAGCATGCGTTTGGAAAATTCAGATCACAAGACTACTACCCGCGTGAACCTGGCCCAGATGGATATGTCATGGCCAGCATTATGGCGAGAATCAATTGCAATCAGCAGCAGCAGCATCCGGCAGCGTCAAGAATGGACTCGCTTCCCTCCCCTCCTTCTCGTGAAATGCTCGAGTCGCAACTGATAAACAGGTTCAACCCCATGATGAATTTATCTGGGGACAGCGATGCCATGTTCCAGAATGCCGATATTTATGACGAACCAGCTGTTCAACATTTCATTGAAGATATTTTGGCTAACGGTGATGGCAATTCGCCTAGTGTGGAAGATTTTATCCGCAACTTGGAACTGGAGTAA

Transcript

rna-XM_065197187.1

GATCCCCACCTTGCCGCCTCAGAAGAGATGAAAGATGGCGCTCTGGAACAAGCTCCAAACTCTCGATGATGAGGCTCGTACAAAGCTTGGAGAAATTTATGGGAGTAATAATTTCCCTTTAGAAGTGAGAGGGATGTTTGCTGAATGGATTGAATCGCAGTCATGGAGTATATTTGATCAGAACATACCAGAACATACCCAAGAGGCAGAGAGTCTTGTGAATGAACTAATCAAAAAGTTAGGGGAAAAATCTCAACAGCAGCCTCATGACTTGATTACTCAAATGAGGTTTAAAGACCTACAGAAGCAAATAAAGgATTTATATCAAAACAACCCTTGGTCCTTAGTCCTTACCATAAAGGAAATACTGACAGCCGAACAAAACCTCCTCATTAAAGCTGAAAAGCCGATGAGCGTGCAATCGCCGATGATGGAGATAGAAACACCAGAAAGCCCATCAATTTTAGATATTGGCCGATTCATTGACGATCTCAAGTCTGCGGCGCAGaaaactgACATGGATTTGAAAAACTATAAACAGCAACAGGAAGATTTTGTCATTCGATACCAGGAGATATGCAAAGTTGACGTGGAAATCAGCAAGGCCACAGAGCGCCGTGATACTAAAGACCAGATGATTATACTGCAAAAGAGGAAAGCTGATATTGAAAAcatgttgaaagaaaaagccCTTGAAATCCTCAATGACCGTGAGGCGATTTTTATACAGCTGGAAAGTCTTAGTTTGAAGATAGAACAGGTTTCCCAAAAGGTTTACCAAGAATTGTTTTTGTGGCGTATGAATCAGCAAAAGTCACTCAGTGGAGGAGACAAGCCAGACCCACTTGACGAATTGCAAAACTGGTTTGAAGCCTTAACAGACACATTGTGGTCCATGTACCAACTGTGCACGCAGTTCAAGTTACTTTTTGATGCTCTGCCAATTATAAGGAATGGCGATGAAAGGGATAAAACCGAAAGGGTCTTAGCAGACGCAGTATCAAGCCTCACAAAGCTAATCCAGAGGTCATTTATTGTTGACAAGCAGCCACCACAGGTTCTGAAAACCCAGACAAAATTTCAAGCGTCTGTTAGattGCTGGTTGGTACCAAGCTCAACTTGCAGCTTAACTGCCCAGAAGTTGTTACAACCATTTTAAGtGAGAAGCAAGCCAAAGAGCTATGCCATGGAAAGACGATAGAAGATACTGGTAGCTGTGGTGAAATTCTGAACAACAGAAGCGTAATGGAGTACGACCAGCAATTGAATGCGCTACATGCagactttaaaaatttgtccttgaagaaaataaagcgTCAGGACAGAAAAGGACAAGAGTCTGTGCTAGAAGCGAAAAGCTGTTTGGTGTTCTCTGCAGCGATAACAATTGGAGGAGAAAAGCTTCCAGTTATGtgTATGTCTGTACCAGTTGTGGTTGTTGTGCATGGCAACCAAGGCCCAAATTCTGAAGCAACGATATTTTGGGacaactttttttcaaacccGGACCGAGAACCTTTCGAGGTGCCAGAGGAAGTCGACTGGGATGAAATGTCCTTCGCTCTTAATGCAAGATGGGCAATGACGACAGAGTGTGACTTGAAAGAAGAGCATTTGGAATATCTAGGCTCGAAATTGTTTCAAAATTGTGAGAAATCCCAAAGCAGCCGTAAGAAGGTATCTTGGCATGCATTTAATAAGGAGCCATTGAAGGGTCGCAATTTTACTTTCTGGGAATGGTTTCATTCAGGAATGGAGGTGGTGAAAAGGCATCTTAAAGATCATTGGAAAGAGGGATATCTGGAGTTCATGTCAAGAGAAGAGGCTCGCAAGAAACTGAATGATATGTGTGTTGGGACGTTTATAATAAGATTCAGTGACGGAGAAGTTGGAGGGGTCAGCATTGCTTGGGTTATTGAGAAAGAAGGGGGAGgCGCTGATATATGGAATGTGCAGCCGTGGACTACGAAGGATTTCAACATCAGATCTCTTGCAGACAGgatCTTTGATTTGGATCTGTTGAAATACGTCTATCCTGGTGTTGAGAAGGAGCATGCGTTTGGAAAATTCAGATCACAAGACTacTACCCGCGTGAACCTGGCCCAGATGGATATGTCATGGCCAGCATTATGGCGAGAATCAAttGCAATCAGCAGCAGCAGCATCCGGCAGCGTCAAGAATGGACTCGCTTCCCTCCCCTCCTTCTCGTGAAATGCTCGAGTCGCAACTGATAAACAGGTTCAACCCCATGATGAATTTATCTGGGGACAGCGATGCCATGTTCCAGAATGCCGATATTTATGACGAACCAGCTGTTCAACATTTCATTGAAGATATTTTGGCTAACGGTGATGGCAATTCGCCTAGTGTGGAAGATTTTATCCGCAACTTGGAACTGGAGTAATCCCAATCAACACGATGGAAACCATTCTATTaaatattagaaaaagttCGATTTGGGAATTGTATCTCATAAAATTATAAGCTGATGGTAGATAAAGATATAATAAttattaactttttctttgtcgtTTGAGACGCAAAACACAATTTGGAATTTCATTAAGGAATTTCATGGTTTCATAAACCAAAGTATTTCTAATATGCCATCTGATAACTTTAGGAAACCTTACCTGATTTCCTCCTGCGAAAAAAGAATTGTGCCTTGCgactaaaaatgaaaggctttgattattgaaatgttttcgtATCAAATATCTGTGGTACAGAGTTGCAAAACTTGGTTGAATTACATTATAGGAGAAAAACAGAAGGAAAACTCCGATCATTAGAATTTGCCGCTTTGTGCTACCCCATgctcaaatgttttcaatctTACCCAGTTTGTCTTCCTTGAGGAAGATCATTGCAGGCAAATTTGTGGTGCTAACGCCTTCCCACACAGTCAGTCAAATACTGTTTGGCACAATGAAACTTGAGGAAGGTACGGTCAAATCGGTTTTATAGCCTGTCGCCCTTTCCCGAAAACGAGGCTAGCCAATGAACATTATTCTCCTCACGTCTAACAAACAACAAAGATACCGCTGAGAGATCCCCCACAGAGATATGATTTCGTTTCTGCCCTTCCACATTAAATATCACGTGATTTAGGTACCTGAATTTGATATTCGttataaactttgttttgatttcatacAAACGTTAAGTTGCTTCAGACAGCAAACgtgtttaatttttagaaaggtAATTAATAGCCTCTGTCTTGTAGTTTTGTATAGTTTAGTTGGTTTGAAAGAGAGACTGTTTTTCGTCATAAAACAGGGAATCTTTCCTGAAATATCTGAGGCATGGCCAGACTGTGTCCATTGAAATAAGTTTAAAGTTATGCTTTGACTTGATATGTATTGAAGAAGATGAGCTTGTCTCTCTTAAAAATGAGAATAGTGCATCTATGGatttatagtttttatttttatcactgcactTGTAACTCGTTTCCGGTATTATCAAAACccgaatttttttttaatttttttgttttcatttctggAATAAAAAGTTGTAGATAAAGCTGCCATAAAGCTGTgtatgaaagtttttgatttcttATCAGAATGA

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003311 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02864 all species →	STAT_bind	STAT protein, DNA binding domain	Domain	Interproscan
PF21354 all species →	STAT_linker	Signal transducer and activator of transcription, linker domain	Domain	Interproscan
PF00017 all species →	SH2	SH2 domain	Domain	Interproscan
PF02865 all species →	STAT_int	STAT protein, protein interaction domain	Domain	Interproscan
PF01017 all species →	STAT_alpha	STAT protein, all-alpha domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036535 all species →	Homologous_superfamily	STAT transcription factor, N-terminal domain superfamily	Interproscan
IPR013799 all species →	Domain	STAT transcription factor, protein interaction	Interproscan
IPR000980 all species →	Domain	SH2 domain	Interproscan
IPR013801 all species →	Domain	STAT transcription factor, DNA-binding	Interproscan
IPR001217 all species →	Family	Transcription factor STAT	Interproscan
IPR012345 all species →	Homologous_superfamily	STAT transcription factor, DNA-binding, N-terminal	Interproscan
IPR048988 all species →	Domain	Signal transducer and activator of transcription, linker domain	Interproscan
IPR008967 all species →	Homologous_superfamily	p53-like transcription factor, DNA-binding domain superfamily	Interproscan
IPR036860 all species →	Homologous_superfamily	SH2 domain superfamily	Interproscan
IPR013800 all species →	Domain	STAT transcription factor, all-alpha domain	Interproscan
IPR015988 all species →	Homologous_superfamily	STAT transcription factor, coiled coil	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11801 all species →	SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0007165 all species →	Biological Process	signal transduction	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0006952 all species →	Biological Process	defense response	Interproscan
GO:0007259 all species →	Biological Process	cell surface receptor signaling pathway via JAK-STAT	Interproscan
GO:0042127 all species →	Biological Process	regulation of cell population proliferation	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
K11224	STAT5B; signal transducer and activator of transcription 5B	-	Transcription factors	ko03000	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 →