Gene detail

Detailed information of BRAKERYMEP00000003168.1 in Astreopora myriophthalma

Genomic Location: BLFK01000093.1:1131533...1146527
NR annotation: XP_020611239.1, short transient receptor potential channel 4-like [Orbicella faveolata]
Species Astreopora myriophthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERYMET00000003168

ATGAAAACACCTTCAACCGATGGTTTTGTTCGTCCACTATGGGTGACCGATCCTCCGATCGAGGGACAGGAATCGTTTTTCGAAGGGGTACCAATGGTTGAGCTAAGCGGTGAAACTGCTCGGTCGATAGAACGGCCGAGGTTTAGGAGCCTCCTTCATAAAGTCAATGAGCAACAAGAAACTAATGGCTTCATGCTGAATCATGAGACCAAACTTGAAGAATCGCTGCTGAAAGCAGTTCAAGAGGGGGACCTTCAAATTATTCAAGTCTTAACTGATCATTTCTTGCAAGTGTTTAATCTAGAAGAACGATACGAGAATTCAGTTGCGACCGCAAGAAAAACTCCTGTCAATTTTCTACCGCTTGTTGTTGCTGCACATTTCGGGAATTACGACGTTCTTAAACTGTTTATATCCAAGGGCTTTAAGTTGGTAAAACCGCACGATGTGCTTTGTAAGTGTGATCATTGCCAAGAAGATTATTTCAGGCAATCGCAAAAACGCCTCGATGTTTACAGAGCTATGGCAAATCCGATGTGGATTTCGCTAACAGGGAGTGATCCATTCTTGACCGCGTTTAAATTGAGTAAAGATTTAAAACGCTCCGCGAAGCAAGAAGACGAGTTCGAAAAAGATTACCTCGCATTGTCGTTGCAATGCAGTCAATTTGCCTTGGGGCTTTTGGATGAATGTAAAACGTCTAAGGAACAGAGAACTGTGCTAAATTTTCCAGGGACGGAGGCCAGTGATGAAGAATTTGCCGAGGAAGCCTTGGGACTGCTTCACAATGCTATCTCTTTCGGGCAAAAAGAGtttgtcgcGCATCCATTCTGTCAGCATCTTCTCATGAGCTCTGTGTTCAGCGGTGTCCCATTCTGGCGCACGCGTGGAATCCCGTTCCGAGTCTTCTACGTCGTGTTTCAAGTGCTGATTTATCCTCTCGTGGCTATTCTGTATTTCTTCTGTCCATTTCTGCGAATAAGCCAAAACATCAAAACGCCGTTTGTAAAATTCATCAACCACACGGCCTCGTTCGTGGTTTTTCTCTCCCTCCTGGCGGCTTCGTCTCATGAGAAATTCGAAATTCGCTTCCGAAAAGTACCATCTGCACTGGAGTGGACCATCTTAATGTGGATTCTCGGAATAGCGTGGGGTGAGTGCAAACAAGTACGGCACGACGGCATGTTAAGATACCTGTCGAGTGGTTGGAATTGGATGGACATGGGAATGATAGTTCTCATCCTAGGCGCTTACTTAGTTTGGTTCGCACGCGCTATTGTGGGACATTTTAGCGACATCGGTCGCTCCACAGACCACTTTGTTCTGAGTGCAGCAGATGGGCTGTATGCTATGGGTGTAATAGCAAGCTTCTTCCGCTTGGTGTACTTGTGCCAGATTAGCCGATACTTGGGTCTCTTGCAGCTCAGCCTTAGTAGAATGGTTCGCGTTATTTTCCAATTTGCATTTATCAGCATTGTGATGTTAATATCGTTTTCTGTTGGTATGACTATGCTGTATTCATCGTCGTTTGAAGCGTATGGCCAGGAGAGACCGCAGAGAAACACCACTGATCCAATAGAGAGTTTAATCAGCAAAGGATATCACAGtttgatcgaaacaatgataacaatgatgTGGGCAAGTTTGGATATGATAACGCTGGACAGTCTGGCTGTGTTCAAGGATCAAAGCCTAATTCAGATATGGACAGCAATCCTGTTTACACTTTATCATGCGGCGTCACTCATCGTCCTACTCAATATGTTGATTGCTATGATGAGCAATTCATACCAACGTGTTGAGGACAACATTGAAACTGAATACAAGTTTGCTCGTGCGCAGTTATGGGCTGATTACATTGGAGATGGTGTGGCTACCCTGCCCCCACCCTTGAATCTCATTCCATCCCCCAAGAGTGTTGTGAGCCGGGTTTGCAGGCTGACGAAAAAGTGTTTCGGAGTGCCTAAAAAGCTGTCTTGCTGCGTAAATGGGCAATTGAGGGTTTATGAAGAGCACAGCATGGACgtagaacaaaagaaacaattatacCAGAATGTGGTCCGAGAACTAATTAGCCGTTACTGGGCAAGACGTCGACTCCAGAAAAGCGCTTCCGACGGCGGCGAAGTCAACGCCGACCAAATGGCTGCCATAACAAGAGTCAAGGAGGAGGTAGCAGATATGTTAAGCGAGATAAGGAACATACTGAAGGCAAATAAAAAGAGTAGAAATCGAGAAAGAATCCTTAGACGCGAGGAGGTTGCTTTTGAGATTGGAGAATCATCGAAGACAAATGGAAGTTTCAGTCACATGGAGCTTTGA

Transcript

BRAKERYMET00000003168

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9QZC1	Short transient receptor potential channel 3 OS=Mus musculus OX=10090 GN=Trpc3 PE=1 SV=2
Q9JMI9	Short transient receptor potential channel 3 OS=Rattus norvegicus OX=10116 GN=Trpc3 PE=2 SV=4
Q13507	Short transient receptor potential channel 3 OS=Homo sapiens OX=9606 GN=TRPC3 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005133 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00520 all species →	Ion_trans	Ion transport protein	Family	Interproscan
PF08344 all species →	TRP_2	Transient receptor ion channel II	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005821 all species →	Domain	Ion transport domain	Interproscan
IPR002153 all species →	Family	Transient receptor potential channel, canonical	Interproscan
IPR013555 all species →	Domain	Transient receptor ion channel domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10117 all species →	TRANSIENT RECEPTOR POTENTIAL CHANNEL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005216 all species →	Molecular Function	monoatomic ion channel activity	Interproscan
GO:0006811 all species →	Biological Process	monoatomic ion transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0005262 all species →	Molecular Function	calcium channel activity	Interproscan
GO:0070588 all species →	Biological Process	calcium ion transmembrane transport	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015279 all species →	Molecular Function	store-operated calcium channel activity	Interproscan
GO:0034703 all species →	Cellular Component	cation channel complex	Interproscan
GO:0051480 all species →	Biological Process	regulation of cytosolic calcium ion concentration	Interproscan
GO:0070679 all species →	Molecular Function	inositol 1,4,5 trisphosphate 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
K04968	TRPC5; transient receptor potential cation channel subfamily C member 5	-	Ion channels	ko04040	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 Astreopora myriophthalma 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 Astreopora myriophthalma, 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 →