Gene detail

Detailed information of ENSQNNP00000025577.1 in Candelabrum cocksii

Genomic Location: chr8:459567...466079
NR annotation: XP_047136011.1, splicing factor 3A subunit 1 [Hydra vulgaris]
Species Candelabrum cocksii · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSQNNT00000026566

atgccgccggccattttgaatgacGAAAATGTGGCCGAACACGAGGTTGTGGAAGACAAAGCTGGGAATGTGCTGGAAAGATCGCAGCAAGATGGTGAACTTTACTCGAAACCGACGGTTGGTATCATCTATCCTCCACCTGAAGTGAGAAATATTGTTGACAGAACTGCAAGCTTTGTTGCAAGGAACGGGCCTGAATTTGAGGATCGTATTCGAGGAAATGAAGCAGACAATCCAAAGTTCAACTTCTTGAATCCAAATGACCCGTATCATGCGTATTATGAACACAAACTGAAAGAATTTCGTGAAGGGGACCCTAGTGAACCGGTTCCTTCTGTTTCTCAAGATAAAGAAATTGCAACTCCAGGAAGTGTTGCCAAGCAAAAGGTAGCGCAGGTCCTTGAGACCATCATTCCCAAAGATCCTCCACCAACATACGAATACATGATTGACCCTCCCACCATCTCTGCAATAGACCTTGATATCGTTCGATTGACAGCTCAGTTTGTGGCGAAGAATGGTAAGGGCTTTCTCACCAATCTCATGACAAGAGAACAGCGAAACTACCAGTTTGACTTCCTTCGGCCTCAGCACAGCTTGTTTCAGTATTTCACGAGATTGGTGGAACAATATACAAAGGTTTTGTTACCACCAGCTGATATTTGTAAAACACTGGAGAAAGAAGTGACCGATTGTTGGAAGATATTAGACAGGGTTAAGTACCGGGTTGAATGGCAGAAATACCAAGAGAGGGAGGTGCGCAAACTCGAAGATGTCAAGGAAAAAGAGAGAATTGCATTTGCGCAGATTGATTGGCATGACTTTGTTGTGGTGGAGACAGTAACCTTTCGGGAAGACGAAGCCTCCAATCTTCCACCACCCGTCACAAAGGATCAGTTGGGTGCTCGCTTGCTTGCGCAGGAACGTTATGATAATGCTCACACCACTGTTAAGGAAAATGTCCAAGGTCAGCAACATCAACGTGAAATTGCGATGGACGTTGTAAACGAAGTCGAAGAAGATCTCTATCAACCATCGTTCCAAGAAGATGATAAAAAACAAGACGAAGAGAAAGCTGGTTCTGATATGGAGGAAGAGAGTGATGAAGACGAACCAGTGCCTCCTCCTCCTCCAAAGGAAATGCCACCTCCAATGGCTCCACCCTCTGGCCTTAGCTCCTCTATTCGTAAAAATTATGACCCCAAAGCAAAGACAAGTTTGAATCAGGCCGGTGATAAGTTTCTTATTTCACCTCTAACTGGTGAAAAGGTGCCTGTGGAATCCATGGCCGCACACAtgaagataaatttgttagaTCCGCGCTGGAAAGAACAAAAGGAGAAGGCAATAGAGGAAAAACGACAGCAAGAGCAAGTGTTTGCTGATGGTGTTCATATTGGTGATACGCTGAAGCAGTTGGCAGAACGACGGTCCGATATCTTTGGAGTTGGGGCAGAAGAAACATTCATCGGTAGAAAGCTGGGAGAAGAGGAAGCTCCTAAGAAAATAGGAGCTGAGATTTGGGACGGCCACACAGCGAGTATGGAACGTACAACCAAACTTGCTCATTCTAACATCACGTTTGAGGACCAGATTAAAGCCATTCATAGATCGAAAGGCTTGCTGCCATCAGAAGATGCTGAGAAGATCGGCCCTTCCATTCCCACTCCCGAACCGACAGTGTTCACTGCCCCTCCGAAAGTTCAACCGCCCCCTCCTCAACTCCCAATGATCATGGCAACTCCGTCATCTACTGTCTCATCAGAGGACAAACCGCGTGCATACATGGATACACTTTCAGCTACCAACACAGCCATGATCTCACAACCGCCGGTTTCTCCTATTATGCCACCAATTCAAACGAATCTTGGCATGGCGCCACCCCCATTGATGCCCCCAAGAATGATGATGCCCCCACCCGCTAATATCCTTGCCCATCCTCAGGTCTCTGCTCCCCCCACCACTTACCTTCAACCACCAGACGAAGCGAGCTTACGTGATGACGGAGAACCAAACTCAAAGCGAGTGAAACTTGACGGACTTGAAGCAGATCTTCTACCCGAGGACATATACTTGCAGCAAAACAGACTTCCCGTCACATTCCGCGTGCAAGTGCCAGAATTGCCGGAGAAACCCGAGTGGCAATGCCAGGGTCAAGTACTTAAAGTCACACTACCATTAAGTGATCAGTGCTCAATGGTCAAAACAAAGGTTTCTGAGATGATAGGAATGCCAACTGGAAAACAAAAGTTGCTTTTATCTAGTTACTACATCAAAGACTCGAACACGCTTGCCTACTACAACTTCTCTTCGTCAACGTTGATCAATATCCAGCTGAAAGAGAGAGGAGGAAGGAAGAAATAG

Transcript

ENSQNNT00000026566

ATTTGTTATGTAGTTTAGAAATTGAATTAATTATAAAATGTTTGCTTTAAAGAAATTCTCTTCTTAAACAATTTACTTTTCGACACACCAGCAACATGGACGGTTTACTGTAAACAGCAGCTTCTTGTATGTGTtaagatataaataaaatgccgccggccattttgaatgacGAAAATGTGGCCGAACACGAGGTTGTGGAAGACAAAGCTGGGAATGTGCTGGAAAGATCGCAGCAAGATGGTGAACTTTACTCGAAACCGACGGTTGGTATCATCTATCCTCCACCTGAAGTGAGAAATATTGTTGACAGAACTGCAAGCTTTGTTGCAAGGAACGGGCCTGAATTTGAGGATCGTATTCGAGGAAATGAAGCAGACAATCCAAAGTTCAACTTCTTGAATCCAAATGACCCGTATCATGCGTATTATGAACACAAACTGAAAGAATTTCGTGAAGGGGACCCTAGTGAACCGGTTCCTTCTGTTTCTCAAGATAAAGAAATTGCAACTCCAGGAAGTGTTGCCAAGCAAAAGGTAGCGCAGGTCCTTGAGACCATCATTCCCAAAGATCCTCCACCAACATACGAATACATGATTGACCCTCCCACCATCTCTGCAATAGACCTTGATATCGTTCGATTGACAGCTCAGTTTGTGGCGAAGAATGGTAAGGGCTTTCTCACCAATCTCATGACAAGAGAACAGCGAAACTACCAGTTTGACTTCCTTCGGCCTCAGCACAGCTTGTTTCAGTATTTCACGAGATTGGTGGAACAATATACAAAGGTTTTGTTACCACCAGCTGATATTTGTAAAACACTGGAGAAAGAAGTGACCGATTGTTGGAAGATATTAGACAGGGTTAAGTACCGGGTTGAATGGCAGAAATACCAAGAGAGGGAGGTGCGCAAACTCGAAGATGTCAAGGAAAAAGAGAGAATTGCATTTGCGCAGATTGATTGGCATGACTTTGTTGTGGTGGAGACAGTAACCTTTCGGGAAGACGAAGCCTCCAATCTTCCACCACCCGTCACAAAGGATCAGTTGGGTGCTCGCTTGCTTGCGCAGGAACGTTATGATAATGCTCACACCACTGTTAAGGAAAATGTCCAAGGTCAGCAACATCAACGTGAAATTGCGATGGACGTTGTAAACGAAGTCGAAGAAGATCTCTATCAACCATCGTTCCAAGAAGATGATAAAAAACAAGACGAAGAGAAAGCTGGTTCTGATATGGAGGAAGAGAGTGATGAAGACGAACCAGTGCCTCCTCCTCCTCCAAAGGAAATGCCACCTCCAATGGCTCCACCCTCTGGCCTTAGCTCCTCTATTCGTAAAAATTATGACCCCAAAGCAAAGACAAGTTTGAATCAGGCCGGTGATAAGTTTCTTATTTCACCTCTAACTGGTGAAAAGGTGCCTGTGGAATCCATGGCCGCACACAtgaagataaatttgttagaTCCGCGCTGGAAAGAACAAAAGGAGAAGGCAATAGAGGAAAAACGACAGCAAGAGCAAGTGTTTGCTGATGGTGTTCATATTGGTGATACGCTGAAGCAGTTGGCAGAACGACGGTCCGATATCTTTGGAGTTGGGGCAGAAGAAACATTCATCGGTAGAAAGCTGGGAGAAGAGGAAGCTCCTAAGAAAATAGGAGCTGAGATTTGGGACGGCCACACAGCGAGTATGGAACGTACAACCAAACTTGCTCATTCTAACATCACGTTTGAGGACCAGATTAAAGCCATTCATAGATCGAAAGGCTTGCTGCCATCAGAAGATGCTGAGAAGATCGGCCCTTCCATTCCCACTCCCGAACCGACAGTGTTCACTGCCCCTCCGAAAGTTCAACCGCCCCCTCCTCAACTCCCAATGATCATGGCAACTCCGTCATCTACTGTCTCATCAGAGGACAAACCGCGTGCATACATGGATACACTTTCAGCTACCAACACAGCCATGATCTCACAACCGCCGGTTTCTCCTATTATGCCACCAATTCAAACGAATCTTGGCATGGCGCCACCCCCATTGATGCCCCCAAGAATGATGATGCCCCCACCCGCTAATATCCTTGCCCATCCTCAGGTCTCTGCTCCCCCCACCACTTACCTTCAACCACCAGACGAAGCGAGCTTACGTGATGACGGAGAACCAAACTCAAAGCGAGTGAAACTTGACGGACTTGAAGCAGATCTTCTACCCGAGGACATATACTTGCAGCAAAACAGACTTCCCGTCACATTCCGCGTGCAAGTGCCAGAATTGCCGGAGAAACCCGAGTGGCAATGCCAGGGTCAAGTACTTAAAGTCACACTACCATTAAGTGATCAGTGCTCAATGGTCAAAACAAAGGTTTCTGAGATGATAGGAATGCCAACTGGAAAACAAAAGTTGCTTTTATCTAGTTACTACATCAAAGACTCGAACACGCTTGCCTACTACAACTTCTCTTCGTCAACGTTGATCAATATCCAGCTGAAAGAGAGAGGAGGAAGGAAGAAATAGAACTTTATTCTGTATTGTTATCTTATAAAAATATCGCGAAAGATGAATAGAAcgtcttttctcttttattttatgataaaATGAAGTATGGACAATCGAAGTATTTAGTCATTTATAGGGTGTATAAGTTATATGTGCGATGACGAAAAGAAAATCCACGAGGAAAGCTACAGCAAAGTTGCCAGATAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A2VDN6	Splicing factor 3A subunit 1 OS=Bos taurus OX=9913 GN=SF3A1 PE=2 SV=1
Q15459	Splicing factor 3A subunit 1 OS=Homo sapiens OX=9606 GN=SF3A1 PE=1 SV=1
Q8K4Z5	Splicing factor 3A subunit 1 OS=Mus musculus OX=10090 GN=Sf3a1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005098 (this species only) · gene tree & orthology
Ubiquitin family	ULD\|UBL\|NEDD8 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00240 all species →	ubiquitin	Ubiquitin family	Domain	Interproscan
PF12230 all species →	PRP21_like_P	Pre-mRNA splicing factor PRP21 like protein	Family	Interproscan
PF01805 all species →	Surp	Surp module	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000061 all species →	Domain	SWAP/Surp	Interproscan
IPR000626 all species →	Domain	Ubiquitin-like domain	Interproscan
IPR035967 all species →	Homologous_superfamily	SWAP/Surp superfamily	Interproscan
IPR022030 all species →	Domain	Splicing factor 3A subunit 1, conserved domain	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan
IPR045146 all species →	Family	Splicing factor 3A subunit 1	Interproscan
IPR035563 all species →	Domain	Splicing factor 3A subunit 1, ubiquitin domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15316 all species →	SPLICEOSOME ASSOCIATED PROTEIN 114/SWAP SPLICING FACTOR-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000381 all species →	Biological Process	regulation of alternative mRNA splicing, via spliceosome	Interproscan
GO:0005686 all species →	Cellular Component	U2 snRNP	Interproscan
GO:0045292 all species →	Biological Process	mRNA cis splicing, via spliceosome	Interproscan
GO:0071004 all species →	Cellular Component	U2-type prespliceosome	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 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
K12825	SF3A1, SAP114; splicing factor 3A subunit 1	-	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 Candelabrum cocksii 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 Candelabrum cocksii, 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 →