Gene detail

Detailed information of OS493_004978-T1 in Lophelia pertusa

Genomic Location: scaffold_10:1673249...1679750
NR annotation: KAJ7374639.1, eukaryotic translation initiation factor 6 [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
Q6GR45	Eukaryotic translation initiation factor 6 OS=Xenopus laevis OX=8355 GN=eif6 PE=2 SV=1
P56537	Eukaryotic translation initiation factor 6 OS=Homo sapiens OX=9606 GN=EIF6 PE=1 SV=1
O55135	Eukaryotic translation initiation factor 6 OS=Mus musculus OX=10090 GN=Eif6 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008296 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01912 all species →	eIF-6	eIF-6 family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002769 all species →	Family	Translation initiation factor IF6	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10784 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 6	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0042256 all species →	Biological Process	cytosolic ribosome assembly	Interproscan
GO:0043022 all species →	Molecular Function	ribosome binding	Interproscan
GO:0000054 all species →	Biological Process	ribosomal subunit export from nucleus	Interproscan
GO:0000460 all species →	Biological Process	maturation of 5.8S rRNA	Interproscan
GO:0000470 all species →	Biological Process	maturation of LSU-rRNA	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0030687 all species →	Cellular Component	preribosome, large subunit precursor	Interproscan
GO:0043023 all species →	Molecular Function	ribosomal large subunit binding	Interproscan
GO:1902626 all species →	Biological Process	assembly of large subunit precursor of preribosome	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
K03264	EIF6; translation initiation factor 6	-	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 OS493_004978-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

53.6Max TPM

21.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.73	33.23
polyp at pH7 6	18	18	31.41	53.56
coral polyp · control treatment	16	16	24.53	41.95
coral polyp · oil and dispersant treatment	16	16	18.50	35.65
coral polyp · oil treatment	16	16	19.11	35.55
coral polyp · dispersant treatment	16	16	14.58	34.14
Polyp	10	10	19.61	34.53

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	-	33.23
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.72
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.01
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.97
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.98
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.60
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.61
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.15
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.33
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.93
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.62
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.87
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.94
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.50
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.19
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.91
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.85
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.56
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.06
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.16
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.91
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.18
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.36
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.17
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.13
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.15
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.88
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.57
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.91
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.66
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.99
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.86
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.29
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.60
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.95
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.42
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.26
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.67
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.95
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.79
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.36
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.30
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.24
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.01
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.46
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.78
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.54
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.45
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.58
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.65
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.09
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.59
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.25
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.88
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.45
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.28
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.94
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.91
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.49
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.12
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.86
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.53
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.21
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.35
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.55
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.60
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.25
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.10
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.80
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.68
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.55
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.76
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.05
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.63
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.78
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.09
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.51
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.34
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.43
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.64
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.14
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.24
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.97
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.09
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.74
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.55
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.87
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.80
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.48
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.07
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.27
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.93
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.03
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.03
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.10
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	34.53
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	27.32
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	26.25
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	22.30
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	18.18
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	16.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	16.20
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.20
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	11.52
SRR7746666	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.