Gene detail

Detailed information of OS493_009321-T1 in Lophelia pertusa

Genomic Location: scaffold_22:1832306...1842813
NR annotation: KAJ7373993.1, Eukaryotic translation initiation factor 3 subunit C, partial [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
Q6PFQ2	Eukaryotic translation initiation factor 3 subunit C OS=Danio rerio OX=7955 GN=eif3c PE=1 SV=1
Q6P1V4	Eukaryotic translation initiation factor 3 subunit C OS=Xenopus tropicalis OX=8364 GN=eif3c PE=2 SV=1
Q4QR58	Eukaryotic translation initiation factor 3 subunit C OS=Xenopus laevis OX=8355 GN=eif3c PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001785 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01399 all species →	PCI	PCI domain	Domain	Interproscan
PF05470 all species →	eIF-3c_N	Eukaryotic translation initiation factor 3 subunit 8 N-terminus	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000717 all species →	Domain	Proteasome component (PCI) domain	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR027516 all species →	Family	Eukaryotic translation initiation factor 3 subunit C	Interproscan
IPR008905 all species →	Domain	Eukaryotic translation initiation factor 3 subunit C, N-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13937 all species →	EUKARYOTIC TRANSLATION INITATION FACTOR 3, SUBUNIT 8 EIF3S8 -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_009321-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_009321-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

61.9Max TPM

27.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	29.48	43.12
polyp at pH7 6	18	18	30.30	47.21
coral polyp · control treatment	16	16	28.85	61.85
coral polyp · oil and dispersant treatment	16	16	25.87	46.76
coral polyp · oil treatment	16	16	33.10	58.78
coral polyp · dispersant treatment	16	16	16.57	31.45
Polyp	10	10	26.94	60.69

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.12
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.38
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.28
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.47
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.20
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.72
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.60
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.72
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.62
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.26
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.05
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.51
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.07
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.57
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.18
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.75
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.25
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.85
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.21
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.65
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.19
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.66
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.34
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.42
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.42
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.02
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.23
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.82
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.55
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.97
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.94
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.63
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.26
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.91
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.85
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.04
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.81
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.22
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.48
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.52
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.95
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.76
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.72
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.75
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.26
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.59
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.68
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.76
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.77
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.28
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.99
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.04
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.46
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.83
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.59
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.26
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.59
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.32
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.18
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.85
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.45
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.97
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.51
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.78
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	56.16
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.62
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.60
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.93
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.41
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.58
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.79
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.12
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.92
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.67
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.20
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.05
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.06
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.26
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.44
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.45
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.88
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.47
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.40
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.40
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.43
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.65
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.65
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.60
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.81
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.63
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.91
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.08
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.96
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	60.69
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	55.86
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	30.36
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	27.63
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	21.60
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	19.37
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	18.62
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	17.55
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.81
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.93

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.