Gene detail

Detailed information of OS493_018003-T1 in Lophelia pertusa

Genomic Location: scaffold_58:1617049...1618953
NR annotation: KAJ7372729.1, Eukaryotic translation initiation factor 3 subunit D [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
A7SMR1	Eukaryotic translation initiation factor 3 subunit D OS=Nematostella vectensis OX=45351 GN=v1g235689 PE=3 SV=1
Q3T122	Eukaryotic translation initiation factor 3 subunit D OS=Bos taurus OX=9913 GN=EIF3D PE=2 SV=1
O15371	Eukaryotic translation initiation factor 3 subunit D OS=Homo sapiens OX=9606 GN=EIF3D PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006560 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05091 all species →	eIF-3_zeta	Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007783 all species →	Family	Eukaryotic translation initiation factor 3 subunit D	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12399 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 7	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003743 all species →	Molecular Function	translation initiation factor activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005852 all species →	Cellular Component	eukaryotic translation initiation factor 3 complex	Interproscan
GO:0006413 all species →	Biological Process	translational initiation	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_018003-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_018003-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

71.3Max TPM

35.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	33.97	45.11
polyp at pH7 6	18	18	38.39	52.89
coral polyp · control treatment	16	16	40.22	60.55
coral polyp · oil and dispersant treatment	16	16	42.63	71.34
coral polyp · oil treatment	16	16	33.13	60.06
coral polyp · dispersant treatment	16	15	30.36	59.79
Polyp	10	9	24.89	35.93

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.11
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.33
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.56
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.80
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.88
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.76
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.72
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.52
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.41
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.40
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.38
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.24
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.64
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.46
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.45
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.58
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.89
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.50
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.30
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.65
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.14
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.60
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.68
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.03
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.50
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.13
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.18
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.93
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.13
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.05
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.35
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.66
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.40
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.99
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.55
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.53
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.77
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.00
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.62
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.64
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.45
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.38
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.35
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.28
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.36
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.78
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.30
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.12
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.12
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.27
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.34
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.54
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.85
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.80
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.17
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.27
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.89
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.87
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.68
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.73
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.91
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.52
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.48
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.92
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.18
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.06
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.61
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.67
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.66
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.89
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.49
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.74
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.95
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.66
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.24
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.18
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.58
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.24
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.58
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.79
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.61
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.60
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.81
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.33
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.31
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.29
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.68
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.62
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.29
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.18
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.17
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.72
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	35.93
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	35.17
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	32.36
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	30.78
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	28.16
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	25.25
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	22.37
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	20.51
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	18.36
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.