Gene detail

Detailed information of OS493_017854-T1 in Lophelia pertusa

Genomic Location: scaffold_58:128205...135646
NR annotation: KAJ7372583.1, translation initiation factor eIF-3b like protein [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A7MB16	Eukaryotic translation initiation factor 3 subunit B OS=Bos taurus OX=9913 GN=EIF3B PE=2 SV=1
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

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006577 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_017854-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR011400 all species →	Family	Eukaryotic translation initiation factor 3 subunit B	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

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

No KEGG orthology assignment for OS493_017854-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_017854-T1 across 110 RNA-seq samples of Lophelia pertusa. 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.

110Samples

110TPM > 0

7Conditions

124.5Max TPM

57.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	41.77	60.99
polyp at pH7 6	18	18	49.03	67.70
coral polyp · control treatment	16	16	69.08	112.20
coral polyp · oil and dispersant treatment	16	16	75.56	124.52
coral polyp · oil treatment	16	16	60.57	112.72
coral polyp · dispersant treatment	16	16	54.74	95.05
Polyp	10	10	50.59	97.72

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.99
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.17
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.92
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.30
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.52
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.89
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.91
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.79
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.13
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.92
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.05
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.13
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.27
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.47
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.05
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.38
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.70
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.29
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.51
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.78
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.46
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.53
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.45
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.39
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.63
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.31
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.22
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.81
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.48
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.28
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.13
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.56
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.17
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.81
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.20
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	105.92
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	100.04
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.54
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.53
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.22
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.54
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.73
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.49
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.25
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.43
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.17
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.54
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.53
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.69
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.51
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	124.52
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	115.63
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.82
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.42
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	84.27
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.28
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	79.30
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.56
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.16
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.10
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.98
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.33
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.60
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.92
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.72
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.72
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	81.21
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	77.44
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.20
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.19
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.74
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	69.98
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.64
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.44
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.85
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.50
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.96
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.49
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.56
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.52
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.74
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	95.05
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.92
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.60
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.79
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.12
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.67
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.60
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.16
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.91
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.92
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.09
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.28
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.36
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.88
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.09
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.42
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	97.72
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	74.26
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	67.76
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	53.28
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	45.13
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	38.26
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	38.25
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	36.01
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	35.67
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	19.59

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 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.