Gene detail

Detailed information of ENSQPTP00000019373.1 in Actinia mediterranea

Genomic Location: chr19:748678...756607
NR annotation: XP_031573029.1, WD40 repeat-containing protein SMU1-like [Actinia tenebrosa]
Species Actinia mediterranea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSQPTT00000023780

tcaaaatccaagatggcgctCGAAGTGGAGTCAGCAGATGTTATCAGGCTTATTCAGCAATTCTTGAAAGAAAACAGCTTACAGAGAACTCTTGCAACATTACAGGAAGAGACAGGCGTCACGTTGAACACAGTAGACAGTGTCGAGAGCTTTATTACTGAAATTAATAGCGGGCACTGGGATACAGTACTGACAGCAATACAGTCACTGAAGTTACCCGACAAGACCTTAATCGATCTTTATGAGCAGATAGTACTTGAGTTAATAGAGCTCCGAGAGCTTGGAGCAGCTCGTTCACTCCTTCGACAGACAGATCCGATGATAATGCTGAAGGCACAACAGGCTGATCGATATTTACACCTTGAAAACATGTTGGCGAAGTCATACTTTGACAGCAGAGAGGCTTATCCTGAAGGTGGCAGTAAAGAAAAGCGAAGAGCAGCAATAGCACAAGCTCTTTCAGGTGAAGTGTCTGTCGTTCCACCTTCACGTCTAATGGCACTGTTAGGCCAGGCTTTGAAGTGGCAGCAATACCAAGGCTTGCTTCCCCCTGGAACGACGATTGACTTGTTTCGAGGGAAAGCTGCCGTAAGAGatgaggaagaagaaaaatatcctACACAGTTGAACAAAATTATCAAGTTTGGAAGCAAGTCTCATCCAGAGTGTGCAAAATTCTCCCCCGATGGACAGTACCTAGTGACCGGCAGTGTTGATGGATTCATTGAAGTATGGAACTTTACGACAGGGAAGATTAGAAAAGATCTAAAATACCAAGCACAGGAGAACTTCATGTTAATGGAACAGAGTGTACTGTGCTTGTGTTTTAGTAGAGATAGCGAGATGTTGGCCACTGGGGGACAAGACGGCAAAATCAAGGTCTGGAAGTTGCAGACGGGTCAATGTCTGAGAAGATTCGAGAGAGCTCACGCCAAGGGTGTAACATGTGTGATGTTCTCTCGTGATGCAAGTCAGTTGTTGAGTGGCTCATTTGACATGACAATAAGGATGCATGGACTCAAATCTGGGAAGACACTAAAGGAGTTCAGAAGCCATACATCGTTTGTTAATGATGTCATCTTCACGTCTGATGCTCACAATATTATAAGCGCAAGCAGTGATGGAACTGTCAAGATCTGGAACATCAAATCCACTGAGTGTTTGCACACATTCAAGCCATCAGTAGGCAGCACCACAACAGACATCACAGTCAACTCAGTCACACTTTTCCCCAAGAATGTGGAGCAGTTTGTTGTGTGTAATCGTTCAAATACTGTGGTGATCATGAACATGCAAGGGCAGATCGTTCGTAGTTTCACAAGTGGTAAGCGTGAAGGTGGTGATTTCGTTAGCTGTATTCTATCACCTCGTGGAGAGTGGATGTACTGTGTAGGGGAAGACATGGTCTTGTATTGCTTCAGCACAACCACAGGAAAACTAGAACAATCCGTACAGGTTCACGAGAAGGATGTCATAGGAATAGCTCACCATCCACATCAGAATTTACTCGCTACGTACAGTGAAGACGGGCAGCTAAAACTGTGGAAACCATAGAAACtatccactacctttttaccAACGTCTATCGGTATCCATGTTGGAAAGAATCCTGAGATAGAGCTGTATTTTCTAGAGGTTTCTAGGACTTTCAAGAAGGGCGTGAAGAGAAATCCAATCGTGATGTACATATGATCCAGACTTCTGGTCAGAAATAGTAACAAACACTCAATCCTGTTGCGTAGCTATGGAAACAGTTTAGAAAAGTAAACAAGCCTCCTATCTAAAAAACCTCAAGGTTATATCTTGAACTAGGTATCCATGGTAACTGATATGAAATGTAACCTGGCCTCACATGGAGCCATATAGAAGGTAACCGCGCCTTCTGCAGGCTtcccgccatcttggaaacaaACAATTTTCATCATAATAACTGTTTTTTTAGCCTTCTATTTGActcaaattttattttctcttaaaaGAAACTGACTGTATTATTTAGTGTATCTTATTTTAATAAACTATTAGTGCTTGTGAACATGTCTTGCTTTTTTATTTGATGGTTTTATGGTTGACCTTTAACGAGCAGCACTTTCTGGTAGCCAACTTTCGCGCCTCACATTGgtatttctcttcttttttctcttatatacactcaataggacgtttgcacgatggcgtcattgacctctactaccagactcccttgcacactttcttttgttcagttaattagtaccaattgtcttactattctcatgagggaatacgaatttaaatgagaaagaaaattcgcgaagtatcttggtagtgggagtcaaatgacgccatcatgcaaacgtcctattgaagaatcgttgtcgggttcagaaacatacaACATAGcctgggggggaggggggggggtactcccctatattcgctatacgggcacgtgccgccaaacagggtatggtat

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q2TBS9	WD40 repeat-containing protein SMU1 OS=Bos taurus OX=9913 GN=SMU1 PE=2 SV=1
Q5ZME8	WD40 repeat-containing protein SMU1 OS=Gallus gallus OX=9031 GN=SMU1 PE=2 SV=1
Q76B40	WD40 repeat-containing protein SMU1 OS=Cricetulus griseus OX=10029 GN=SMU1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006235 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17814 all species →	LisH_TPL	LisH-like dimerisation domain	Domain	Interproscan
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR006595 all species →	Domain	CTLH, C-terminal LisH motif	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR006594 all species →	Conserved_site	LIS1 homology motif	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR045184 all species →	Family	WD40 repeat-containing protein SMU1	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22848 all species →	WD40 REPEAT PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0008380 all species →	Biological Process	RNA splicing	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	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
K13111	SMU1; WD40 repeat-containing protein SMU1	-	Spliceosome	ko03041	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 →