Gene detail

Detailed information of OS493_001441-T1 in Lophelia pertusa

Genomic Location: scaffold_3:1632107...1655465
NR annotation: KAJ7381319.1, Eukaryotic translation initiation factor 4E type 2 [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
Q8BMB3	Eukaryotic translation initiation factor 4E type 2 OS=Mus musculus OX=10090 GN=Eif4e2 PE=1 SV=1
O60573	Eukaryotic translation initiation factor 4E type 2 OS=Homo sapiens OX=9606 GN=EIF4E2 PE=1 SV=1
Q22888	Eukaryotic translation initiation factor 4E-4 OS=Caenorhabditis elegans OX=6239 GN=ife-4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005595 (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
IPR001040 all species →	Family	Translation Initiation factor eIF- 4e	Interproscan
IPR023398 all species →	Homologous_superfamily	Translation Initiation factor eIF- 4e-like	Interproscan
IPR019770 all species →	Conserved_site	Eukaryotic translation initiation factor 4E (eIF-4E), conserved site	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
GO:0005737 all species →	Cellular Component	cytoplasm	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_001441-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

224.8Max TPM

72.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	86.70	120.42
polyp at pH7 6	18	18	92.65	155.50
coral polyp · control treatment	16	16	56.42	69.68
coral polyp · oil and dispersant treatment	16	16	47.51	107.57
coral polyp · oil treatment	16	16	62.85	117.37
coral polyp · dispersant treatment	16	16	44.39	84.70
Polyp	10	10	139.70	224.81

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	-	120.42
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	119.36
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	111.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	111.75
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	107.59
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	107.11
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	86.27
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	85.31
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	83.51
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	80.75
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	80.44
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.85
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.82
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.29
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.59
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.05
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.53
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.16
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	155.50
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	151.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	124.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	123.39
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	115.09
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.65
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	96.30
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.21
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	85.93
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	83.93
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.60
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.64
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.51
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.92
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.27
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.42
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.39
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.53
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.68
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.45
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.05
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.92
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.51
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.15
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.43
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.56
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.14
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.23
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.90
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.17
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.45
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.25
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.45
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.43
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.36
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.55
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.40
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.21
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.56
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.87
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.34
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.94
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.12
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.07
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.81
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.89
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.97
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.81
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	117.37
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.47
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.38
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.14
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.77
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.30
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.14
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.80
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.63
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.53
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.33
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.98
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.47
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.18
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.86
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.35
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	84.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.91
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	58.88
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.14
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.46
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.18
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.45
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.32
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.28
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.82
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.47
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.31
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.37
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.24
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.51
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	224.81
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	218.40
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	161.48
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	157.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	134.66
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	132.23
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	131.06
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	98.72
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	82.47
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	55.68

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.