Gene detail

Detailed information of OS493_004002-T1 in Lophelia pertusa

Genomic Location: scaffold_8:1297982...1303495
NR annotation: KAJ7387039.1, Eukaryotic translation initiation factor 4H [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
Q1JPH6	Eukaryotic translation initiation factor 4H OS=Bos taurus OX=9913 GN=EIF4H PE=2 SV=1
Q5RBR8	Eukaryotic translation initiation factor 4H OS=Pongo abelii OX=9601 GN=EIF4H PE=2 SV=1
Q15056	Eukaryotic translation initiation factor 4H OS=Homo sapiens OX=9606 GN=EIF4H PE=1 SV=5

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004759 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23236 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005844 all species →	Cellular Component	obsolete polysome	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_004002-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_004002-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

224.0Max TPM

90.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	52.82	70.50
polyp at pH7 6	18	18	55.24	74.55
coral polyp · control treatment	16	16	133.23	171.15
coral polyp · oil and dispersant treatment	16	16	118.03	224.02
coral polyp · oil treatment	16	16	120.81	175.49
coral polyp · dispersant treatment	16	16	102.99	201.88
Polyp	10	10	40.41	70.56

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.50
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.32
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.51
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.44
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.61
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.57
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.92
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.21
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.08
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.96
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.51
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.50
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.31
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.18
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.04
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.73
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.42
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.03
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.55
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.26
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.71
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.70
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.95
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.34
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.25
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.65
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.43
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.64
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.32
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.17
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.09
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.19
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.75
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.52
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	171.15
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	170.71
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	168.73
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	166.23
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	165.86
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	158.00
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	139.50
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	136.12
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	132.78
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	130.99
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.69
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.07
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	102.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.68
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.27
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.21
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	224.02
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	160.65
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	154.63
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	152.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	138.30
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	136.74
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	129.99
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.47
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.95
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	94.96
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	94.46
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.28
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.75
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.33
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.57
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	175.49
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	167.06
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	145.57
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	140.79
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	139.60
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	136.07
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	135.50
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	135.11
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.23
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.22
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.57
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	104.95
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	100.99
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	74.94
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.71
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.14
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	201.88
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	183.98
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	133.13
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	130.69
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	129.08
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	121.21
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	100.98
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	100.02
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	95.48
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	92.33
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.90
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.37
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.75
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.63
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.63
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	70.56
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	53.68
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	49.37
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	44.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	36.14
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	34.11
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	34.10
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	29.74
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	29.67
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	22.44

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.