Gene detail

Detailed information of OS493_009298-T1 in Lophelia pertusa

Genomic Location: scaffold_22:1571881...1590493
NR annotation: KAJ7373970.1, Eukaryotic translation initiation factor 3 subunit C [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
Q3SYW6	Eukaryotic translation initiation factor 3 subunit C OS=Bos taurus OX=9913 GN=EIF3C PE=2 SV=1
Q6P1V4	Eukaryotic translation initiation factor 3 subunit C OS=Xenopus tropicalis OX=8364 GN=eif3c PE=2 SV=1
B5ME19	Eukaryotic translation initiation factor 3 subunit C-like protein OS=Homo sapiens OX=9606 GN=EIF3CL PE=1 SV=1

Gene family

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

Pfam domain

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

InterPro

InterPro term	Type	Description	Source
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_009298-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_009298-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

62.5Max TPM

32.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	31.06	52.68
polyp at pH7 6	18	18	31.85	43.68
coral polyp · control treatment	16	16	37.39	58.12
coral polyp · oil and dispersant treatment	16	16	39.41	55.98
coral polyp · oil treatment	16	16	33.78	62.54
coral polyp · dispersant treatment	16	16	33.44	55.14
Polyp	10	10	17.46	31.85

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.68
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.43
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.37
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.81
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.92
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.75
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.74
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.76
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.52
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.82
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.71
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.31
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.22
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.86
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.68
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.80
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.41
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.41
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.82
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.55
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.39
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.78
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.55
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.63
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.78
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.12
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.81
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.93
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.80
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.53
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.16
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.03
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.17
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.12
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.67
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.31
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.48
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.49
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.38
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.01
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.62
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.98
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.77
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.18
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.97
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.31
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.98
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.88
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.56
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.65
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.78
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.64
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.29
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.46
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.86
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.12
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.65
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.38
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.19
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.58
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.57
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.88
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.99
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.05
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.53
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.41
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.40
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.75
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.65
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.58
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.85
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.27
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.74
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.75
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.14
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.43
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.21
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.06
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.09
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.54
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.52
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.54
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.13
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.93
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.13
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.67
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.01
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	31.85
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	25.08
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	23.38
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.78
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	18.63
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	15.20
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.94
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	11.30
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.22
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.19

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.