Gene detail

Detailed information of alvinactis_v1_g391 in Alvinactis idsseensis sp. Nov.

Genomic Location: chr_1:7084964...7104306
NR annotation: XP_020917462.1, splicing factor 3B subunit 1 isoform X1 [Exaiptasia diaphana]
Species Alvinactis idsseensis sp. Nov. · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

alvinactis_v1_g391

ATGGCGACGTTAGCGAAGGCTCCGACTACTCACGAAGAAATCGAGAAGCAAATTCAAGAGCTTCAGGCTCGTAGGACCGGCGGTGCAGAGCAGACTAAAGGTTTCGATGATGGCGAACGTGTTGGTTTGGGTTCTGCTGGTCGTTTTGATACAGACATCTATGGATCTGAAGACAAGTATGCAGGATATGTCCCTTCAATTGCAGCCAATGAACACGAAGAGGATGATGATGATTATGCTACAACCTCAATCATGCAACCTGGAAAACGTCAGTCTTACACAGCACCCCTGGCAGTACTTAATGATATGACTAAGGGAGAACAGGTGGACCCTTTTGCAGAACACAGACGGCAGACTATTGCTGAAAGAGAAGATGAATACAGAGCAAGGAGACGACAGATGATTATTTCCCCACCAAGACATGATCCATTTGCTAACGGTGGCAAGACACCCGACCCCTCCCATCTCAAGAATGTCAGGACTTACTCAGATGTCATGCAGGAGCAGGATCTTAGACGTGATCAAGTTGAGTTGGTTAAGCAAATACAAGAGAAAGCCAAGTCTGGGGAATTGCACACCACTCAAGCTGCACAAACAAAGCCAGAGCGGAAACGTCGTCGTTGGGACCAGCAAGCAGGAGGAGATGACACTCCTGCAAAAAAGAAATCTGGTTGGGACCAAGCAGAGGTATCAACACCATCGATGAGTCGCTGGGATGAGACACCAGGAAAACCTAAAGGATCTGAGACACCTGGTGTTACTCCACATAGATCTGGTTCTGAGACCCCAGGGGCTACACCAAGCACAAGAATCTGGGAAGCCACTCCTAGTcatactacacctggacatgctacacctggacatactacacctggacatgctacaccagggaatactacaccAGGAATGGCATCATCACGAAGAAATCGTTGGGATGAAACACCTAAATCAGAAAGAGGAGAAACTCCTGGTCATTCTACTCCAGGATGGGCAGAGACCCCCAGGACAGATAGAACTGGTGCAGAGACACCAGGAGCAACCCCAACACCTGCCAGCAAAAGGCGATCAAGGTGGGATGAGACACCTGCTAGTCAAATGGGTGGTTCCACTCCTATGGTTGGTTCTAGTGGCGTCACCCCAGCAGGTGCTGCTGCTATGCAGATGCAGACACCAACACCAGGTCAGCTTGTGTCTATGACCCCAGAACAAATGCAAGCATATAGATGGGAGAGAGAAATTGATGAGAGAAACAGACCTCTGTCAGATGAAGAACTGGATACCTTATTCCCTAAAGAAGGATACAAGGTATTGGATCCTCCTACAGGATATCAACCAATAAGAACACCTGGTCGACGTCTGACTGCCACGCCCACTCCTGCTGGTGGATCAGGATTCTATATGCAGCAAGAAGATCATTCAGCTAAAGTAATTGATGACCAACCACCTGGAAATCTTCCTTACCTCAAACCTGATGATGTTCAATACTTTGACAAACTATTGGTTGATGTTGACGAAAGTACACTAAGTCCTGAGGAGCTTAAAGAAAGAAAGATCATGAAGCTTTTACTCAAGATAAAGAATGGCACTCCACCAATGAGAAAGGCCGCATTAAGACAGATTACAGACAAGGCCAGGGAGTTTGGGGCTGGGCCATTATTTAATCAGATTTTACCACTACTCATGTCTCCTACACTGGAAGATCAGGAGCGTCACTTGTTAGTGAAAGTCATTGATCGTATTTTGTACAAGCTAGATGACTTGGTCAGACCATTTGTACACAAGATTCTCGTCGTCATTGAACCACTGCTGATTGATGAAGATTACTATGCAAGAGTAGAGGGTAGAGAAATTATTTCTAACTTGGCCAAGGCTGCAGGGTTGGCTACAATGATTTCTACAATGAGACCTGATATTGACAACATTGATGAATATGTCCGTAATACCACTGCAAGAGCTTTTGCAGTTGTTGCATCTGCTTTGGGTATCCCTTCTCTGTTACCATTCTTAAAGGCTGTGTGTCGCAGTAAAAAGTCCTGGCAGGCAAGACACACTGGTATCAAGATTGTCCAGCAGATTGCCATCCTTATGGGTTGTGCTATTTTGCCACATCTTAGAAATCTTGTGGAGATTATTGAACATGGTCTTATTGATGAACAGCAGAAGGTACGCACTATTACTGCTCTTGCTTTGGCTGCTTTAGCTGAAGCTGCAACTCCCTATGGCATTGAATCATTTGATAGCGTACTCAAACCTCTATGGAAAGGTATCAGGCAGCACAGAGGAAAGGGTTTGGCTGCTTTCTTAAAAGCCATTGGCTACTTGATACCTCTGATGGATGCCGAGTATGCGAACTACTACACCCGTGAAGTCATGATCATCTTGATTCGTGAGTTTCAAAGTCCTGATGAGGAAATGAAAAAGATTGTGCTGAAGGTGGTGAAGCAGTGTTGTGCAACTGATGGTGTAGAACCATCATATATCAAACAGGATATCCTGCCTGACTTCTTTAAACATTTCTGGCAGCACAGAATGGCTTTGGATAGAAGaaattaccgtcagcttgtggacaccacGGTTGAGTTGGCAAATAAAGTTGGTCCATCTGAAATCATTAATCGTGTTGTTGATGACTTGAAAGATGAGAATGAACAATACAGAAAGATGGTCATGGAGACTATTGAAAAGATTATGGGAAACCTTGGATCAGCTGATATTGATTCAAGACTTGAGGAACAGCTGATTGATGGCATATTGTATGCATTCCAAGAACAGACACAAGAGGACATTGTCATGTTGAATGGTTTTGGTACGGTGGTCAATGCATTGAGTAAGAGAGTGAAACCATACTTGCCTCAGATTTGTGGTACAATTCTTTGGCGTTTAAACAATAAATCAGCCAAGGTCAGACAGCAAGCAGCAGATCTCATCTCTAGGATTGCTCAGGTCATGATGACTTGTGGAGAGGAAAAACTGTTAGGGCATCTTGGTGTTGTCTTGTATGAGTACCTTGGCGAAGAATACCCGGAAGTACTGGGAAGTATCCTTGGAGCACTTAAGGCTGTAGTCAATGTTATTGGGATGAACAAGATGACCCCACCCATCAAAGATCTACTACCTAGACTTACACCCATCCTCAAAAACAGGCATGAAAAGGTGCAGGAAAACTGTATTGACCTGGTTGGTCGTATTGCTGATCGTGGAGCTGAACATGTTGGTGCCAGAGAATGGATGAGAATTTGCTTTGAATTGCTTGAGTTACTCAAGGCACACAAGAAGGCCATTAGGAGAGCTACAGTCAATACATTTGGTTATATTGCAAAGGCTATTGGTCCACAAGATGTATTAGCAACTCTCCTTAACAATCTGAAAGTCCAGGAGAGGCAGAACCGTGTGTGTACAACCGTGGCCATTGCCATTGTTGCAGAGACTTGCTCGCCATTTACAGTCTTACCAGCACTAATGAATGAATACAGAGTCCCTGAACTTAACGTCCAAAATGGTGTCCTGAAGTCACTTTCATTTCTGTTTGAGTACATTGGAGAAATGGGAAAAGATTATATTTATGCCGTCACATCGTTATTAGAAGATGCTCTTATGGACAGAGATCTGGTTCATCGACAAACAGCATGTTCAGCTATCAAGCACATGTCACTTGGTGTGTTTGGTCTTGGTTGTGAAGATGCATTGTGTCATCTAATGAACTATGTGTGGCCAAATATCTTTGAGACTTCACCTCATGTAATCAACGCTGTTATGGAGGCTGTAGATGGATTAAGAGTAGCTTTAGGACCAGCAAAAACATTACAATATTGTATGCAGGGTTTGTTTCATCCCGCAAGAAAAGTTCGCGATGTTTATTGGAAAATATATAATAATCTTTATATTGGATCTCAGGATGCTCTAGTAGCTGCTTATCCAACAGCTCTGAATGATGAGAAGAATACTTATGTACGCTCAGAGATGATGTATTTTGTGTAG

Transcript

alvinactis_v1_g391

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O75533	Splicing factor 3B subunit 1 OS=Homo sapiens OX=9606 GN=SF3B1 PE=1 SV=3
Q99NB9	Splicing factor 3B subunit 1 OS=Mus musculus OX=10090 GN=Sf3b1 PE=1 SV=1
O57683	Splicing factor 3B subunit 1 OS=Xenopus laevis OX=8355 GN=sf3b1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004661 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08920 all species →	SF3b1	Splicing factor 3B subunit 1	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015016 all species →	Domain	Splicing factor 3B subunit 1	Interproscan
IPR034085 all species →	Domain	TOG domain	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR038737 all species →	Family	Splicing factor 3B subunit 1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12097 all species →	SPLICING FACTOR 3B, SUBUNIT 1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000245 all species →	Biological Process	spliceosomal complex assembly	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005686 all species →	Cellular Component	U2 snRNP	Interproscan
GO:0005689 all species →	Cellular Component	U12-type spliceosomal complex	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
K12828	SF3B1, SAP155; splicing factor 3B subunit 1	-	Chromosome and associated proteins	ko03036	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 Alvinactis idsseensis sp. Nov. 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 Alvinactis idsseensis sp. Nov., 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 →