Gene detail

Detailed information of OS493_017549-T1 in Lophelia pertusa

Genomic Location: scaffold_56:1646302...1651967
NR annotation: KAJ7385172.1, Gem-associated protein 5 [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
Q54IY5	Component of gems protein 5 OS=Dictyostelium discoideum OX=44689 GN=gemin5 PE=3 SV=1
Q62623	Cell division cycle protein 20 homolog OS=Rattus norvegicus OX=10116 GN=Cdc20 PE=1 SV=2
Q9JJ66	Cell division cycle protein 20 homolog OS=Mus musculus OX=10090 GN=Cdc20 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003885 (this species only)
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12894 all species →	ANAPC4_WD40	Anaphase-promoting complex subunit 4 WD40 domain	Repeat	Interproscan
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR024977 all species →	Domain	Anaphase-promoting complex subunit 4-like, WD40 domain	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan
IPR052640 all species →	Family	WD repeat domain-containing protein Gemin-5	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46362 all species →	GEM-ASSOCIATED PROTEIN 5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000387 all species →	Biological Process	spliceosomal snRNP assembly	Interproscan
GO:0003730 all species →	Molecular Function	mRNA 3'-UTR binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0032797 all species →	Cellular Component	SMN 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_017549-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_017549-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

102TPM > 0

7Conditions

18.8Max TPM

3.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	2.53	4.60
polyp at pH7 6	18	14	2.28	4.76
coral polyp · control treatment	16	16	4.36	18.84
coral polyp · oil and dispersant treatment	16	16	3.78	15.90
coral polyp · oil treatment	16	16	3.69	7.05
coral polyp · dispersant treatment	16	16	4.56	9.80
Polyp	10	8	1.04	2.31

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.60
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.51
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.43
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.37
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.17
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.05
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.99
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.90
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.88
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.53
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.40
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.97
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.57
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.91
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
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.76
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.31
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.52
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.16
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.14
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.08
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.91
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.74
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.73
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.41
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.18
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.16
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.11
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.91
SRR11359501	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
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	18.84
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.72
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.49
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.84
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.82
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.28
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.70
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.65
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.14
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.00
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.95
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.58
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.12
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.02
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.81
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.75
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.28
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.45
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.26
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.60
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.47
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.02
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.70
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.69
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.40
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.33
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.78
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.72
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.53
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.81
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.05
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.29
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.22
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.91
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.81
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.58
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.06
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.87
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.27
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.25
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.42
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.26
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.23
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.07
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.80
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.80
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.36
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.53
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.37
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.68
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.28
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.25
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.02
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.65
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.27
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.11
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.80
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.43
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.81
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.31
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.96
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.36
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.32
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.16
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.15
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.64
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.50
SRR7746667	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.