Gene detail

Detailed information of ENSQPTP00000028999.1 in Actinia mediterranea

Genomic Location: chr4:4278034...4289504
NR annotation: XP_031554883.1, TBC1 domain family member 23-like isoform X2 [Actinia tenebrosa]
Species Actinia mediterranea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSQPTT00000035590

atggcggaagGTGGAGGTATTGAAGACGATGGATGGCACACAGACTTAATTCTAGCGCTGTCCAAACAAAAGGATCCCGAGCGACTTCGTGAACTTTGCCGCGGACGTAAAATACCTGCCGAAAACAGAGCTGATATTTGGAAGGTTTGCCTCAACGTAGTAGGAAAGCCAGATGCTTTGTCAACATGGGATGGAATGTTGGATTTGAACGAACAAGATATGATCAGAGATGATTGCAAGCGACAAGCCGGAAAGCTTCATTTGTCTGATGATGACATTGACGAAGTTGCTCGAGAAATGGAAAGCATCATAACATTTTACTGTAAATCAAGAAATGAAAAGTACAGAACTACAAGTGGCCTCACGGAACTGTTAGCACCATTAATGATGCTTGACATACCCACCAGTGATGTTTATAATTGTTTTTATGCTTTGCTCTATAAATTTATACCAAGgGATTGTGTGAGGGATGGAAAACCCTTTCATCTATTCAGACTGCTTCTACAGTACCATGATCCTGAACTATGTTCATTTTTAGACTCTAGAAAATTATCACCAGATTCATATTGTCAAACATGGATCCGGAGTCTAATGGTAGCAGTATGTGAAGATGATGTGATCCGTGCTTTATGGGATGTTTATCTACTTGAATCAGATCCTTTTCTTatcttctttttatctttaGTAATGATCGTAAATGCCAGAGATCAAGTTTTTGAACTTAAATCAGCGAGTAAAGCAGATATCTTAGAAATGATAGCATTAATACCAGGCCAGCTAGAAGCTGATGATATTGAAGACTTTTGTTCCCTTGCTCAGTATTATGCAACAAGAACTCCTCAGTCTTTTAGAAAGGACTACTACAGTCAGTTGTTTGGTGTAAAGACTATCAACTCTAACAGTATTTCACAAGCTCTTTGTCTCCCAGTGTCTGTGTCAGAGTTGCTAGGGGCCAATCAGTCTAATCACAAAGATGGGGTGAGGTTTTTCGTGGTAGACTGCAGACCAGCTGAACAATACAACAGTGGGCACCTACCAACAGCGTTTCACCTGGATGCAAACCTGATGTTACAAGCCCCTTCAGAGTTTGCAACAGCAGCCAAGGCCCTATTTGCCACCCAAAAACAATCACTAGCAGCCGGATCAGTAGCAGGAGGGGAACACCTTTGTTTTATGGGGTCAGGACGAGAAGAAGAGGACCAGTATGTACACATGGTCATCGCTAACTTCTTACAGCGCAAAGCAAAGTATGTCAGCCTGGCTCGTGGTGGATATCAGACTCTGCACGAGACGTTGTCTGATGATTTATCAACTGGTCTGGCAGATCACTCACTGCAAAGATGTATTGTATGCACCCCTGAAGCCTATTCTGAAGATGAGAGTTATCACGAATTATCGAGAGGAGGAGACCAAAGTCCGTCCGATGGACGAACTGGTCTTGTTGGTATGCTGTCATCTAAACTAATGTCCAAGGGAGCCAacgttaaagaaaaaataggtcattttatcGCAGAGTCAAGCCAACCAGTGGAAAGGCATGTGAGCAGTACAGACAAACAAAGTAAACTATATAGAAACGTTCAACCAGTATTCAGCATAGAcgacgatgacgatgaaggAGATGCTTGCAGTGTTTCAAGCTCTGAAGATGAAAATCGCAAAGAATCAGTTAATCTGGAGACATGGTTGAAAAGAAAGGACGTTTTTGCCTCATTTGAATGTAATGAGGTGCTTTCCCGTGGTCACCTAGCACCCAGTTACATCCTCATTATGGAAGTCCACATGTATGTACTGCGAGAAATCTCTAAGCGACCTGGCTGGGCACACATCCAGCACAGACATCACCTTGCCGACATCCTTAAGATAACCTCAAAAAGAAAACACCCTGAACTAATAACATTCAAGTATGACGCAGGCAACCTAGAGGACTCAGCGATCAAGTCTGCAGAGAGATACCTTATTCCCAATTCCCAGAAAGCTACCAAGAAAATCAAGGAAAGAATCTTAAAGGTCATTggtgaatga

Transcript

ENSQPTT00000035590

gatgacgtatccaaaatggcggaagGTGGAGGTATTGAAGACGATGGATGGCACACAGACTTAATTCTAGCGCTGTCCAAACAAAAGGATCCCGAGCGACTTCGTGAACTTTGCCGCGGACGTAAAATACCTGCCGAAAACAGAGCTGATATTTGGAAGGTTTGCCTCAACGTAGTAGGAAAGCCAGATGCTTTGTCAACATGGGATGGAATGTTGGATTTGAACGAACAAGATATGATCAGAGATGATTGCAAGCGACAAGCCGGAAAGCTTCATTTGTCTGATGATGACATTGACGAAGTTGCTCGAGAAATGGAAAGCATCATAACATTTTACTGTAAATCAAGAAATGAAAAGTACAGAACTACAAGTGGCCTCACGGAACTGTTAGCACCATTAATGATGCTTGACATACCCACCAGTGATGTTTATAATTGTTTTTATGCTTTGCTCTATAAATTTATACCAAGgGATTGTGTGAGGGATGGAAAACCCTTTCATCTATTCAGACTGCTTCTACAGTACCATGATCCTGAACTATGTTCATTTTTAGACTCTAGAAAATTATCACCAGATTCATATTGTCAAACATGGATCCGGAGTCTAATGGTAGCAGTATGTGAAGATGATGTGATCCGTGCTTTATGGGATGTTTATCTACTTGAATCAGATCCTTTTCTTatcttctttttatctttaGTAATGATCGTAAATGCCAGAGATCAAGTTTTTGAACTTAAATCAGCGAGTAAAGCAGATATCTTAGAAATGATAGCATTAATACCAGGCCAGCTAGAAGCTGATGATATTGAAGACTTTTGTTCCCTTGCTCAGTATTATGCAACAAGAACTCCTCAGTCTTTTAGAAAGGACTACTACAGTCAGTTGTTTGGTGTAAAGACTATCAACTCTAACAGTATTTCACAAGCTCTTTGTCTCCCAGTGTCTGTGTCAGAGTTGCTAGGGGCCAATCAGTCTAATCACAAAGATGGGGTGAGGTTTTTCGTGGTAGACTGCAGACCAGCTGAACAATACAACAGTGGGCACCTACCAACAGCGTTTCACCTGGATGCAAACCTGATGTTACAAGCCCCTTCAGAGTTTGCAACAGCAGCCAAGGCCCTATTTGCCACCCAAAAACAATCACTAGCAGCCGGATCAGTAGCAGGAGGGGAACACCTTTGTTTTATGGGGTCAGGACGAGAAGAAGAGGACCAGTATGTACACATGGTCATCGCTAACTTCTTACAGCGCAAAGCAAAGTATGTCAGCCTGGCTCGTGGTGGATATCAGACTCTGCACGAGACGTTGTCTGATGATTTATCAACTGGTCTGGCAGATCACTCACTGCAAAGATGTATTGTATGCACCCCTGAAGCCTATTCTGAAGATGAGAGTTATCACGAATTATCGAGAGGAGGAGACCAAAGTCCGTCCGATGGACGAACTGGTCTTGTTGGTATGCTGTCATCTAAACTAATGTCCAAGGGAGCCAacgttaaagaaaaaataggtcattttatcGCAGAGTCAAGCCAACCAGTGGAAAGGCATGTGAGCAGTACAGACAAACAAAGTAAACTATATAGAAACGTTCAACCAGTATTCAGCATAGAcgacgatgacgatgaaggAGATGCTTGCAGTGTTTCAAGCTCTGAAGATGAAAATCGCAAAGAATCAGTTAATCTGGAGACATGGTTGAAAAGAAAGGACGTTTTTGCCTCATTTGAATGTAATGAGGTGCTTTCCCGTGGTCACCTAGCACCCAGTTACATCCTCATTATGGAAGTCCACATGTATGTACTGCGAGAAATCTCTAAGCGACCTGGCTGGGCACACATCCAGCACAGACATCACCTTGCCGACATCCTTAAGATAACCTCAAAAAGAAAACACCCTGAACTAATAACATTCAAGTATGACGCAGGCAACCTAGAGGACTCAGCGATCAAGTCTGCAGAGAGATACCTTATTCCCAATTCCCAGAAAGCTACCAAGAAAATCAAGGAAAGAATCTTAAAGGTCATTggtgaatgaaaaaatggttGCAACGATGAATGAGTGTACTGACTAGTCATGAGAGATATGTCAAGAAGTAATCCATACATGAGAATATCTCTTAAAAAGATAGCATGAATACGAAGATGGGACGTCAAGTTTAGTGGAATAGTTATCGGAGATGAAATTAAGTACTCTCAtacgattgccatgggaaaaCTCAAAGCAGGTTATATAGCCTGTTTTTGTCAATGCAAATGCCAGTATATTTTCTGTAGCTGTCATCTAGCTGCTTACTAATATTTAATAAGAACTAGCGTGGAGAGAAATCCACTTAAACATATGAACAATGATACGAAAGAAAACTAGCAAACTAATACCTTTGATGAAGGATAGTAGTGTGCAAGAAATAACCAATCCAATTATTGAACTCCACACCAGTAAAGGACCATAGCAGTATTCTCAATAGCCTTCTTTTACATAATTAGGGTACTATAGTTCTTCCAGTACAAACCTTATTACCCACTTTATATTCTGTAGATTTTgttagaaaacaaaaaaatcatactAAATGGGATGATATAGTCTAAAAATCCTATCCAGTGGATatatttattggataacagcatcaatagatccactggataaggatttgtccattggatagtgctatccatcCTTCATATAACTGGGCACAGGAGGTTATGTTGTATCCTTAGAAAAAAGAGATTGATTTTACTAGATACTGTTAtcacaaaaagaaaatcaaag

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5F415	TBC1 domain family member 23 OS=Gallus gallus OX=9031 GN=TBC1D23 PE=2 SV=1
Q5R8I6	TBC1 domain family member 23 OS=Pongo abelii OX=9601 GN=TBC1D23 PE=2 SV=1
Q9NUY8	TBC1 domain family member 23 OS=Homo sapiens OX=9606 GN=TBC1D23 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005845 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00566 all species →	RabGAP-TBC	Rab-GTPase-TBC domain	Family	Interproscan
PF19430 all species →	TBC1D23_C	TBC1 domain family member 23 C-terminal	Domain	Interproscan
PF00581 all species →	Rhodanese	Rhodanese-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000195 all species →	Domain	Rab-GAP-TBC domain	Interproscan
IPR035969 all species →	Homologous_superfamily	Rab-GAP-TBC domain superfamily	Interproscan
IPR036873 all species →	Homologous_superfamily	Rhodanese-like domain superfamily	Interproscan
IPR045799 all species →	Domain	TBC1 domain family member 23, C-terminal domain	Interproscan
IPR001763 all species →	Domain	Rhodanese-like domain	Interproscan
IPR039755 all species →	Family	TBC1 domain family member 23	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13297 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0042147 all species →	Biological Process	retrograde transport, endosome to Golgi	Interproscan
GO:0099041 all species →	Biological Process	vesicle tethering to Golgi	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
K22555	TBC1D23; TBC1 domain family member 23	-	Membrane trafficking	ko04131	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 Actinia mediterranea 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 Actinia mediterranea, 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 →