Gene detail

Detailed information of OS493_034015-T1 in Lophelia pertusa

Genomic Location: scaffold_279:271548...280351
NR annotation: KAJ7376559.1, Dynein regulatory complex subunit 6 [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
Q8CDU4	F-box and leucine-rich repeat protein 13 OS=Mus musculus OX=10090 GN=Fbxl13 PE=1 SV=2
Q8NEE6	F-box and leucine-rich repeat protein 13 OS=Homo sapiens OX=9606 GN=FBXL13 PE=1 SV=3
Q9QZH7	F-box/LRR-repeat protein 20 OS=Rattus norvegicus OX=10116 GN=Fbxl20 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004479 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 adaptor Cullin RING\|F-box · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12937 all species →	F-box-like	F-box-like	Domain	Interproscan
PF08457 all species →	Sfi1	Sfi1 spindle body protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001810 all species →	Domain	F-box domain	Interproscan
IPR036047 all species →	Homologous_superfamily	F-box-like domain superfamily	Interproscan
IPR039588 all species →	Family	F-box only protein 4	Interproscan
IPR032675 all species →	Homologous_superfamily	Leucine-rich repeat domain superfamily	Interproscan
IPR013665 all species →	Domain	Sfi1 spindle body	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16008 all species →	F-BOX ONLY PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0019005 all species →	Cellular Component	SCF ubiquitin ligase complex	Interproscan
GO:0031146 all species →	Biological Process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	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_034015-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_034015-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

36.9Max TPM

11.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.17	35.66
polyp at pH7 6	18	18	15.50	36.93
coral polyp · control treatment	16	16	12.11	35.97
coral polyp · oil and dispersant treatment	16	16	10.35	30.15
coral polyp · oil treatment	16	16	10.17	16.76
coral polyp · dispersant treatment	16	16	7.85	16.74
Polyp	10	10	7.13	11.50

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	-	35.66
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.35
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.29
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.66
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.32
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.16
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.59
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.10
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.82
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.18
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.14
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.06
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.89
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.88
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.14
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.62
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.44
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.93
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.10
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.39
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.97
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.28
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.74
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.27
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.62
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.29
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.96
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.40
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.52
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.18
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.11
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.01
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.56
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.97
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.47
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.47
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.88
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.52
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.40
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.76
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.21
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.13
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.92
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.30
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.79
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.72
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.15
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.81
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.76
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.97
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.36
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.99
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.94
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.94
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.31
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.05
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.35
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.62
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.60
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.72
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.52
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.76
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.08
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.53
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.15
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.97
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.96
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.59
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.33
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.01
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.39
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.31
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.47
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.45
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.10
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.74
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.21
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.67
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.32
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.55
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.45
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.22
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.87
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.28
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.96
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.93
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.60
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.44
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.16
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.81
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.45
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.50
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.99
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.88
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.66
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.64
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.98
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.71
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.64
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.81
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.47

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.