Gene detail

Detailed information of OS493_028344-T1 in Lophelia pertusa

Genomic Location: scaffold_162:785687...788799
NR annotation: KAJ7326086.1, hypothetical protein OS493_028344 [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
Q6NU27	Eukaryotic translation initiation factor 4E type 3-B OS=Xenopus laevis OX=8355 GN=eif4e3-b PE=2 SV=1
Q6GR08	Eukaryotic translation initiation factor 4E type 3-A OS=Xenopus laevis OX=8355 GN=eif4e3-a PE=2 SV=1
Q28ET8	Eukaryotic translation initiation factor 4E type 3 OS=Xenopus tropicalis OX=8364 GN=eif4e3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007427 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01652 all species →	IF4E	Eukaryotic initiation factor 4E	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR023398 all species →	Homologous_superfamily	Translation Initiation factor eIF- 4e-like	Interproscan
IPR001040 all species →	Family	Translation Initiation factor eIF- 4e	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11960 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 4E RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000340 all species →	Molecular Function	RNA 7-methylguanosine cap binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003743 all species →	Molecular Function	translation initiation factor activity	Interproscan
GO:0006413 all species →	Biological Process	translational initiation	Interproscan
GO:0016281 all species →	Cellular Component	eukaryotic translation initiation factor 4F complex	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
K03259	EIF4E; translation initiation factor 4E	-	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_028344-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

108TPM > 0

7Conditions

50.8Max TPM

18.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.11	24.19
polyp at pH7 6	18	17	15.42	28.58
coral polyp · control treatment	16	16	26.84	50.77
coral polyp · oil and dispersant treatment	16	16	25.92	42.06
coral polyp · oil treatment	16	16	20.52	35.65
coral polyp · dispersant treatment	16	16	16.33	27.46
Polyp	10	9	7.26	16.80

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.19
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.82
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.05
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.41
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.37
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.32
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.06
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.91
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.82
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.74
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.99
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.67
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.50
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.43
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.92
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.34
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.58
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.18
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.56
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.26
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.57
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.26
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.65
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.74
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.80
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.33
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.82
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.49
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.15
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.77
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.26
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.59
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.34
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.68
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.76
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.42
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.40
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.33
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.24
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.31
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.44
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.81
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.34
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.89
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.84
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.77
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.96
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.99
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.32
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.60
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.20
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.10
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.87
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.39
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.32
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.12
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.65
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.53
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.25
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.02
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.58
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.49
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.26
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.52
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.28
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.04
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.74
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.89
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.40
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.83
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.46
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.42
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.20
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.97
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.60
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.25
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.23
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.21
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.90
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.77
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.50
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.08
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.10
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.23
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.98
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.41
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	16.80
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.04
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	10.36
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.05
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.77
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.77
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.22
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.78
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.83
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.