Gene detail

Detailed information of ENSBQFP00000018399 in Heliopora coerulea

Genomic Location: JASJOG010000035.1:55128...74521
NR annotation: XP_028395481.1, eukaryotic translation initiation factor 3 subunit B-like [Dendronephthya gigantea]
Species Heliopora coerulea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSBQFT00000020517

ATGGCGAACGAGGTTGAGGAGGAAAGTAAAAATCTTTCCGAAGACGACGAAAATGAAGAGATTAACGGTACAGAGGTGGATGAAGAGGAAGACGAGTCACAGTTTGATGATCCAGACGGATTTGTTGATTCAATAAGTGACGAAGAACTTCTGGGTGATATTCTAGACAAAAAGCCAGTCCTTGAGCATGGCATAGATGCCATTATAGTAGTTGATAATGTTCCTATTGTTGGCCAAGATcgacttgagaaactgaaaaatgttattaaaaaagtcttttccaaatttggtaaaattattaatgaattctACCCAGAAGAGAATGGCAAGACAAAAGGATATATCTTTATTGAATATTCAAATCCCAAAGATGCTGCACAAGCTGTGAATATAGCAAATGGTTATAAGCTGGATAAACATCATATTTTTATAGTTAGTCCATTCACATCATTTGATAGTATTTTGGAACTACAAGAGGAATGGAGTCCTCCTGAGAAGGAGCCATATGAAGACAAGGGCAACTTACGTTCATGGCTTCTTGATGGTGATTGCAATGACCAGTATTCAGTGATACATGCTGGAGGAGACAAAGTTGATATATTTGTCAACACTTCAACTGAACCAATTCTGGTTAAAGGACGTCCAGGTTGGACAGAGACATATGTCCGCTGGTCACCTCGGGGGACTTACCTTGCAACATTTCATAAACAAGGTATTGCACTGTGGGGAGGAGATGAGTATAATCGTATTGGCAAATTTGGCCACCAAGGAGTACAAATGATTGATTTCTCACCTTGTGAAAGATATATCGTGACATTCAGTCCACTGCCAGATACAGCCAGTGACCCTCAGAGTATAATTATTTGGGATGTAAGAACAGGAGCTAAGAAAAGAGCATTTCAATGTGGAGACAACTCTCGTTGGCCAATTTTTAAGTGGAGCCATgatggaaaatattttgctCGTATCAGAGATGAAGCCATTAGCATTTACGAGACTCCGtCTTTCGGGTTGCTGGACAAGAAAAGCGTCAAGGTTCCTAGTATAAGGGAGTTTGCCTGGTCCCCCGGGGATAATATGATATCATTCTGGGTGCCAGAAATCAAAGACACGCCAGCTCGTGTGACGATCATGAAGATTCCCAGTCGACAGGAATGCCGAGTGAAAAACTTATTTAATGTAGCCACGTGTAAAATGTATTGGCAAAACAAAGGAGACTACCTCTGTGTGGTTGTGGATCGGTATACTAAGAGTAAAAAGGCTCTTCATTATAACCTGGAGATATTTCATCTGAGGGAGAAGCAAATCCCCGTGGACACCTTGGAACTAAAAGAGGCTGTTAGTGCATTTGCGTGGGAACCTCATGGTGACAAGTTCGCCATCATTCATGGCGAAAATCCAAAGATAAATGTTAGTTTTTATTCCTGCCACAAGGGTGGACGAACAACCCTACTAAAAACCTTTGAGAAGAAACAGGTTAATAGTATATTCTGGTCTCCACGTGGACAGTTTTGCGTCTTGGCGGGCCTTCGCAACATGAGCGGTGCCTTAGAGTTTTACGATCTCAATGAAGTAACATGTATGAATGTTGGAGAGCATTTTACAGCAACGGACGTGGAGTGGGATCCATCTGGACGTTATGTTTCGACATCTGTTAGCTGGTGGGCGCAGAAGGTGGATAATGGTTACTATATTTGGTCATTTCAAGGCAAATTACTTCAAAGACATGCAATCAGTCAGTTTTGTCAGATGCTTTGGAGACCTCGCCCGCCGACGCTGCTATCGGAGGATCAAGTACAGaaaataaaattagaaatCAAGAAATaccataaaatgtttgaaaataaagACCGAATGAGTCAGAAGAAGGCATCTAAAGAATTGATTGAGAAACGTCGGCGTTTAATGAGTGAGTTTATGGCATACCGACAGAGGAAAAGTGATGAATACGCGGAACAGGAAACTGAACGTCGTGAGTTGCGCAAAGGTTGCGAGGAGTTAGAGGAAGAGGTTGATGACTTTGAAGAGGAAACTGTAGAATTCTTTATTAAAGAGGAAGAAACCATTGTGGAGTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q4G061	Eukaryotic translation initiation factor 3 subunit B OS=Rattus norvegicus OX=10116 GN=Eif3b PE=1 SV=1
Q8JZQ9	Eukaryotic translation initiation factor 3 subunit B OS=Mus musculus OX=10090 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
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species

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
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR034363 all species →	Domain	eIF3B, RNA recognition motif	Interproscan
IPR011400 all species →	Family	Eukaryotic translation initiation factor 3 subunit B	Interproscan
IPR013979 all species →	Domain	Translation initiation factor, beta propellor-like domain	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:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
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

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.

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000018399 across 37 RNA-seq samples of Heliopora coerulea. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

37Samples

37TPM > 0

6Conditions

179.6Max TPM

82.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	17	80.98	96.12
polyp and skeleton · 31C, 3week	6	6	63.33	77.97
polyp and skeleton · 28C, 3week	6	6	106.64	179.56
polyp and skeleton · 26C, 3week	4	4	84.37	117.88
polyp and skeleton · 28C, 24hr	2	2	61.95	64.98
polyp and skeleton · 31C, 24hr	2	2	99.19	152.21

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	96.12
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	93.85
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	91.96
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	90.61
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	89.82
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	88.88
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	88.15
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	87.79
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	84.92
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	82.15
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	80.42
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	74.26
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	72.33
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	69.12
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	63.97
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	63.95
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	58.31
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	77.97
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	68.93
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	67.87
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	57.94
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	57.71
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	49.54
SRR12578067	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	179.56
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	151.27
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	93.65
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	86.13
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	82.89
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	46.35
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	117.88
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	111.75
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	76.36
SRR12587801	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	31.48
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	64.98
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	58.93
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	152.21
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	46.17

Source: CnidoSite RNA-seq expression matrices (HCOER_TPM, StringTie quantification over 37 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Heliopora coerulea 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	14	ENSBQFP00000014215	0.813869501449129
Negatively correlated	89	ENSBQFP00000043327	-0.762574971694752

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Heliopora coerulea, 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.	ready	open →
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 →