Gene detail

Detailed information of OS493_021856-T1 in Lophelia pertusa

Genomic Location: scaffold_86:1036402...1038825
NR annotation: KAJ7384443.1, Elongator subunit elp4 [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
Q5XG58	Elongator complex protein 4 OS=Xenopus laevis OX=8355 GN=elp4 PE=2 SV=1
Q566Y1	Elongator complex protein 4 OS=Danio rerio OX=7955 GN=elp4 PE=2 SV=2
Q96EB1	Elongator complex protein 4 OS=Homo sapiens OX=9606 GN=ELP4 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006371 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05625 all species →	PAXNEB	PAXNEB protein	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR008728 all species →	Family	Elongator complex protein 4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12896 all species →	PAX6 NEIGHBOR PROTEIN PAXNEB	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0002098 all species →	Biological Process	tRNA wobble uridine modification	Interproscan
GO:0033588 all species →	Cellular Component	elongator holoenzyme complex	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008023 all species →	Cellular Component	transcription elongation factor 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

No KEGG orthology assignment for OS493_021856-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_021856-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

89TPM > 0

7Conditions

7.2Max TPM

1.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	11	0.93	2.90
polyp at pH7 6	18	10	1.07	2.69
coral polyp · control treatment	16	16	3.26	5.84
coral polyp · oil and dispersant treatment	16	14	1.78	4.18
coral polyp · oil treatment	16	15	2.58	7.15
coral polyp · dispersant treatment	16	15	2.53	5.42
Polyp	10	8	1.01	2.74

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.90
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.15
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.92
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.73
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.61
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.34
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.30
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.89
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.63
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.60
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.69
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.47
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.46
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.08
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.05
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.02
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.63
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.42
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.26
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.13
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.84
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.55
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.42
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.91
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.91
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.91
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.26
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.82
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.31
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.69
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.51
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.37
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.00
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.18
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.75
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.82
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.32
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.28
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.83
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.42
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.37
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.59
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.51
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.34
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.15
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.20
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.23
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.91
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.38
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.69
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.40
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.23
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.07
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.86
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.70
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.51
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.27
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.04
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.68
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.42
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.34
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.90
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.82
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.32
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.16
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.56
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.53
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.87
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.71
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.48
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.24
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.26
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.74
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.93
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.55
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.44
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.08
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.79
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.50
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.11
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
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.