Gene detail

Detailed information of OS493_005730-T1 in Lophelia pertusa

Genomic Location: scaffold_12:251296...255337
NR annotation: KAJ7339337.1, hypothetical protein OS493_005730 [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
Q6IWL4	TNF receptor-associated factor 6 OS=Danio rerio OX=7955 GN=traf6 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000128 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21363 all species →	TRAF3_RING	TNF receptor-associated factor 2/3/5, RING domain	Domain	Interproscan
PF02176 all species →	zf-TRAF	TRAF-type zinc finger	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR049440 all species →	Domain	TNF receptor-associated factor 3/5, RING domain	Interproscan
IPR013010 all species →	Domain	Zinc finger, SIAH-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR001293 all species →	Domain	Zinc finger, TRAF-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10131 all species →	TNF RECEPTOR ASSOCIATED FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0033209 all species →	Biological Process	tumor necrosis factor-mediated signaling pathway	Interproscan
GO:0070534 all species →	Biological Process	protein K63-linked ubiquitination	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_005730-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_005730-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

56.3Max TPM

16.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.50	35.76
polyp at pH7 6	18	18	13.49	26.91
coral polyp · control treatment	16	16	19.42	36.65
coral polyp · oil and dispersant treatment	16	16	8.99	16.44
coral polyp · oil treatment	16	16	12.83	27.02
coral polyp · dispersant treatment	16	16	20.19	56.30
Polyp	10	10	18.25	43.41

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	-	35.76
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.33
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.01
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.55
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.45
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.07
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.43
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.13
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.75
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.55
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.37
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.78
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.32
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.80
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.80
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.68
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.08
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.07
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.91
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.82
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.54
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.82
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.88
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.51
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.48
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.25
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.88
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.45
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.05
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.75
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.34
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.88
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.97
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.48
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.07
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.37
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.71
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.01
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.27
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.89
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.24
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.38
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.08
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.85
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.98
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.44
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.38
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.16
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.88
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.47
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.44
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.11
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.37
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.95
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.39
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.37
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.99
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.79
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.07
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.97
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.71
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.10
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.86
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.78
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.02
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.65
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.83
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.27
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.85
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.75
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.76
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.62
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.47
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.86
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.97
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.27
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.26
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.01
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.76
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.98
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.30
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.56
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.45
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.09
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.04
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.51
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.56
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.82
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.94
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.71
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.84
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.72
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.14
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	43.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	34.30
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	24.81
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	20.11
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.49
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.94
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.28
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.72
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.21

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.