Gene detail

Detailed information of ENSOFVP00000034138.1 in Cyphastrea salae

Genomic Location: chr8:3136132...3141679
NR annotation: XP_020615971.1, retinoic acid receptor RXR-alpha-like isoform X2 [Orbicella faveolata]
Species Cyphastrea salae · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSOFVT00000037045

GTTGTCGCCGCCTGTTGCGTAATGTGAACTTTTCAGTTTTTGAGCTACAGAAGCCATAATCTGGCTTTTTGAAGTGTTATTCAAAGTCTATGGCAGCCTTCAAACATAAGCAACTACGTCATTATTCAAAAGTGGTTCTCGTGTTACGTTTGGGTCTACTTTTAATGCCAGTTTAGGACCAATTAACAAAATGGCTTCCTCCAGGATTTTAATTTTCAGAGGGCACAGTGCTACAAATTTGTAGGCGCGAAAATCGTGCGAAGATGACAGAGAAAGAAGATGAAAGCGAGAAGTGGTGTGCTGTATGCAGTGACAGTTCCTCTGGCTACCATTATGGAGCAAACACTTGCGAGGGGTGCAAGAGTTTCTTCAAAAGAACTGTTCAAAAAGATCTGCTGGAAAAGTACGAATGCAGCGGCAATGAAGATTGCCCTGTTGACAAACAGTCCCGTGCCAAGTGTCAATTCTGCAGGCTACAGAAGTGCTTCACAGTGGGGATGGTCGCAGAAGgtgtgagaaaagaaaaaaggcgTGGAGGACGATCATTCTATCCCTTGAAAAAGCACAAAAGTCAGGAAGAAACTCAAACTTCTTCAAATGAAGATCCCAACATTACATATTGCTCAGAGCTCATTGCAAAACTAATGAACAGTAATCCAAGCATTATCCCCCCTGGTGAGGCACTTGCGAACTCGAGGGAAGCTGTTATTACAGAGAGCAGAGAAGGAATACTGACAAGATTGTCGAATGCAATCACAAAAGAGCTGTACTTTATTGTTGAGTGGGCCAAACTTGTCCCAGGATTTGATCAACTTTGTCGAAAGGATCAGATTGCTTTGTTGACTGCAGGCGGCATGGAATTAATTGTGTTCCGACTCATTTACAGGTCTATTCCTTATAAGGAGCATGTTTACATGAACACCACTACCCTTCTCGTGAGAGAAGATTGTTACAGTGTGCTCAATGAAGAAATAGTTGACATGATTCTGGATGTGGTTGATCGACTTCGACCATTGGCTATGGATGACGTTGAGTTTGCTTGTTTGAAGACCATTCTCTTAGCTGACCCAGAGACACCAGGACTCACTGACAAGATTGCTGTTGGCACACTACAAGGGTCATTTCTAGCAGCTCTTAAAGAGCATATGGAATCAACATACCCTGATCATTCTGGACGATTTGCAAAGCTACTTCTCCGTCTTCCAGCTCTGCGGGATGTATGTACCAAGGGCTACCAGTATTTTTTGCTTGTGCGAGCTAAGCTGGAGGGTGAAATTCCCATGTCAACTTTACTGCAAGAAATGTTTCAATCTGCAAGATTTTAGGCAGTGTTTACTACTCATGCCCAACTCTGCAGGGCAAGATTTTAGAGAGCATTTACTACTCATGCCCACCCTTGTGGGGTTTCAATATCCAATGATACAAAGTTTTATAAACATGTTTTTCACCCAAGTAAAACTGACAAAAATGTTGGTTGTACAGGGTAAATCTAATAGCATTCATCATGCACACTCAATCTTCTTACAGTCTATTTGCACATGTTGTTGTTAGAATATAAATTATTGTGCTCTGGACAAAATTAAATAGAACCCAGTGGTACATACACATGAATGTCTCCCTACAGGTTAAGGGAGTTGTGTACCTGAAGaagagagggagagagaaaaAAGATAACATTACAGGCATATCCTAAAACTTTCACCATGCTAGGGATCTTCTAATGGCATGACTCATTCACCCACCTCCCCCTACCCACCACCCACCACCTCCTCCCCTATCCTCTACATTAACCAATTTGGTTAGTTTTGTTATGTGTGCCAAAATAATCAATTTGATGATTTAATTGGTAGTATAATGTATTTTGCAAATCATGGCGACAAAAATATGTGCACCATTAGCTTGGTTGTAATTACATTTGCAGCAAAGGCTTAGGAAATCCAAAAATATAGAATCATATGCAATAACCTTTTAGACATTTGAAAGTTAAAGTTTagttttaagtttaagtttagcCTGGTTGTACTTGTGAGAGGTTTAGTAAAAAAATCAAGGCGGGTTACTGTTGTGACTGAGCGAAAAACTACAGTCAAGCACTAGAAAAAATTACTGTGGTATAGGGTAGGAATATATAGAAAGTACAGATGTTAATATTATGGAAACTGTTCATGAAAATAATTATAGATTTTATAGTAAAAAGACTCTTTGTATCAAATAATAAAATACTTCAGAAAAGCTTGC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P51128	Retinoic acid receptor RXR-alpha OS=Xenopus laevis OX=8355 GN=rxra PE=1 SV=1
P28700	Retinoic acid receptor RXR-alpha OS=Mus musculus OX=10090 GN=Rxra PE=1 SV=1
Q05343	Retinoic acid receptor RXR-alpha OS=Rattus norvegicus OX=10116 GN=Rxra PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000188 (this species only) · gene tree & orthology
Transcription factor family	ESR-like · all TF in this species
Transcription factor family	Miscellaneous · all TF in this species
Transcription factor family	NGFIB-like · all TF in this species
Transcription factor family	RXR-like · all TF in this species
Transcription factor family	SF-like · all TF in this species
Transcription factor family	THR-like · all TF in this species
Transcription factor family	GCNF-like · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00105 all species →	zf-C4	Zinc finger, C4 type (two domains)	Domain	Interproscan
PF00104 all species →	Hormone_recep	Ligand-binding domain of nuclear hormone receptor	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000536 all species →	Domain	Nuclear hormone receptor, ligand-binding domain	Interproscan
IPR001628 all species →	Domain	Zinc finger, nuclear hormone receptor-type	Interproscan
IPR050200 all species →	Family	Nuclear hormone receptor family NR3 subfamily	Interproscan
IPR003070 all species →	Family	Nuclear receptor subfamily 4 group A member 1-3	Interproscan
IPR013088 all species →	Homologous_superfamily	Zinc finger, NHR/GATA-type	Interproscan
IPR035500 all species →	Homologous_superfamily	Nuclear hormone receptor-like domain superfamily	Interproscan
IPR001723 all species →	Family	Nuclear hormone receptor	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48092 all species →	KNIRPS-RELATED PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0043565 all species →	Molecular Function	sequence-specific DNA binding	Interproscan
GO:0000790 all species →	Cellular Component	chromatin	Interproscan
GO:0004879 all species →	Molecular Function	nuclear receptor activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0034056 all species →	Molecular Function	estrogen response element binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA 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

No KEGG orthology assignment for ENSOFVP00000034138.1.

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 Cyphastrea salae 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 Cyphastrea salae, 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 →