Gene detail

Detailed information of BRAKERNUSP00000004018.1 in Montipora cactus

Genomic Location: BLFO01000310.1:1968096...1995151
NR annotation: XP_027039360.1, eukaryotic translation initiation factor 3 subunit B-like [Pocillopora damicornis]
Species Montipora cactus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERNUST00000004018

ATGGCGGACGAAAAGGAATTGGATGAAAAGGCGGCTAATAGCGattcagaagaagaagatgacGAAGAGGAAGAAATGGCCAATGGAAGAAACGATGTCGGAGGCGACGAGTCGGAGTTTGATGATCCAGAGGGCTTTGTAGACGATATTACGGACGAAGAGCTTTTGGGAGATATCTTGCAAGAAAAGCCAGTGGAAGTCGGGGGAACAGACTGTATAATTGTGGTTGATAATGTGCCTGTCATCCCACCAGACCGACTGGAAAAGCTAAAAAATGTTATCCGCAAGGTTTTTTCCAAGTTTGGGAAGATAATCACTGAGCACTATCCACAGGATGAGAATTTACATACTAAAGGCTATATCTTCCTGGAATTTTCCAATGCAAAAGATGCGGCACAAGCAGTCAAAACTGCCAATGGCTACAAGTTAGACAAGCACCATATATTTGCTGTCAATCACTTTGAGGATTTTGACAGATTAGCAAGTCTAACAAAGGATTGGGAAGCACCTACCAAACAGCCATATGTTGAACAGGAAAACTTGAGGTCATGGCTTTTAGATCAAGATTGTAATGACCAGTACTCTGTGATTCATGGTGGAGGAGACAAAGTTGCAATAATGTGGAACACTATCCAAGAATCAATACTTTGTAAAGAAAGAATGAACTGGACTGAAACATATGTACGATGGTCTCCCAGAGGCACTTACTTATCTACCCTTCATCATCAAGGTATAGCTCTTTGGGGAGGAGAAGAATTCAAAAGGCTCATGAGGTTTAGCCATCCTGGTGTTCAGCTTATAGACTTTTCTCCTTGTGAAAGGTATTTGGTAACTTTTAGTCCCTTAGCAGATAATCCTGATGATCCACagGCTATTGTTATTTGGGATATACGATCTGGGACCAAAAAGAGAGGATTTTTATGTGGAGACCAGTCTCAGTGGCCAGTGTTTAAGTGGAGTGCAGAGGGCAAGTATTTTGCCCGGCTAGGAGAGGACAGCATTAGCATATATGAAACACCTTCATTTGGTCTCTTAGAGAAAAAAAGCTTAAAGATCCAAGGTATAAAAGATTTTGCATGGTCACCAACTGAGAATGTCATAGCTTTTTGGGTTCCTGAGTACAAAGACACTCCTGCGCGTGTAACACTGATGGAAATTCCAAGCAGAAAAGAGATCCGTGTAAAGAATTTGTTTAACGTGTCTgagTGCAAGTTGTTTTGGCAGAATAAAGGAGATTATCTTGGTGTAAAAGTGGATAGGTACACCAAAAGCAAAAAGgGCCTGTATTACAACCTTGAATTGTTCCGCGTTCGAGAGCGGGAGAttcctgttgatgttgttgaaATGAAAGAGGTTGTCAGTGCATTTTCTTGGGAACCTGGTGGCAGTAAATTTGCAGTCATTCATGGGGAAAGTCCAAGAATATCAGCTAGCTTTTACAGCATGGATAAACAACGAAGTGCAGCTCTTTTAAAAACATTTGAGAAAAAGCAAGTCAACAGTATATTTTGGTCACCAAATGGACAATTTTGCATTCTAGCTGGTCTTAGAAATATGAATGGTGTTCTAGAATTTTATGACACTTCTGATGTAGTTTGCATGAATCAAGGAGAGCATTTTATGGCAACGGACGTGGAGTGGGATCCTACGGGCCGATATGTGGCCACCTCTGTCAGTTGGTGGGCACATAAGGTGGATAATGGTTACTATATCTGGTCATTTCAAGGGAAGCTGCTTCAGCGTCACGCATTGGATCAATTCTGTTCGCTTTTGTGGAGACCTAGGCCACCGAGCCTTTTGTCAGATGCTGATATAAAGAACGTCAAGAAGGACATCAAGAGATTTCAGCGCATGTTTGAAGTCAAGGATCGAATGAGCCAGTCACGGGCCTCAAAGGAGCTGATTGAACGGCGGCGCAGCAAGATGAAAGAATTTCAGGGTTACAGGCAGAAAAAGAACAGCGATTATGCACAGCAAAAGCCACAGCGCTTGGAATTACGTAACGGTGTTGAAACAGATGAGCTGGATAGCAATGCGGAGGAGTTTGAGGATGAGTCTGTTGAGTTCTTTGTTAAAGAAGAGATAACCGAAGTGGAGGAGTAG

Transcript

BRAKERNUST00000004018

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8JZQ9	Eukaryotic translation initiation factor 3 subunit B OS=Mus musculus OX=10090 GN=Eif3b PE=1 SV=1
Q4G061	Eukaryotic translation initiation factor 3 subunit B OS=Rattus norvegicus OX=10116 GN=Eif3b PE=1 SV=1
P55884	Eukaryotic translation initiation factor 3 subunit B OS=Homo sapiens OX=9606 GN=EIF3B PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006412 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08662 all species →	eIF2A	Eukaryotic translation initiation factor eIF2A	Repeat	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR013979 all species →	Domain	Translation initiation factor, beta propellor-like domain	Interproscan
IPR011400 all species →	Family	Eukaryotic translation initiation factor 3 subunit B	Interproscan
IPR034363 all species →	Domain	eIF3B, RNA recognition motif	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14068 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 EIF3 -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003743 all species →	Molecular Function	translation initiation factor activity	Interproscan
GO:0005852 all species →	Cellular Component	eukaryotic translation initiation factor 3 complex	Interproscan
GO:0006413 all species →	Biological Process	translational initiation	Interproscan
GO:0031369 all species →	Molecular Function	translation initiation factor binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid 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
K03253	EIF3B; translation initiation factor 3 subunit B	-	Translation factors	ko03012	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 Montipora cactus 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 Montipora cactus, 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 →