Gene detail

Detailed information of OS493_003951-T1 in Lophelia pertusa

Genomic Location: scaffold_8:728915...735521
NR annotation: KAJ7386989.1, hypothetical protein OS493_003951 [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
Q9WTV0	Guanine nucleotide-exchange factor SEC12 OS=Rattus norvegicus OX=10116 GN=Preb PE=1 SV=2
Q9WUQ2	Guanine nucleotide-exchange factor SEC12 OS=Mus musculus OX=10090 GN=Preb PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006227 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · 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
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR045260 all species →	Family	Guanine nucleotide-exchange factor Sec12-like	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23284 all species →	PROLACTIN REGULATORY ELEMENT BINDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003400 all species →	Biological Process	regulation of COPII vesicle coating	Interproscan
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005096 all species →	Molecular Function	GTPase activator activity	Interproscan
GO:0009306 all species →	Biological Process	protein secretion	Interproscan
GO:0030176 all species →	Cellular Component	obsolete integral component of endoplasmic reticulum membrane	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14003	PREB, SEC12; prolactin regulatory element-binding protein	-	Membrane trafficking	ko04131	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_003951-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

109TPM > 0

7Conditions

18.1Max TPM

8.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	6.44	9.68
polyp at pH7 6	18	18	7.32	14.57
coral polyp · control treatment	16	16	10.25	16.17
coral polyp · oil and dispersant treatment	16	16	11.01	15.54
coral polyp · oil treatment	16	16	8.81	14.35
coral polyp · dispersant treatment	16	16	9.91	18.10
Polyp	10	9	3.96	7.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.68
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.41
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.97
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.64
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.54
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.43
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.69
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.87
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.94
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.72
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.52
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.33
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.20
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.97
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.64
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.02
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.76
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.57
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.41
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.19
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.51
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.38
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.97
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.12
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.85
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.76
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.59
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.41
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.07
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.81
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.77
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.64
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.83
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.21
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.17
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.19
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.53
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.79
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.43
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.29
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.10
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.09
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.92
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.09
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.19
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.67
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.85
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.83
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.54
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.75
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.56
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.17
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.96
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.81
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.06
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.01
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.39
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.98
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.77
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.84
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.18
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.79
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.67
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.35
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.58
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.25
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.19
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.87
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.09
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.92
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.19
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.72
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.34
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.69
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.59
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.27
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.46
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.10
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.97
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.63
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.68
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.15
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.58
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.15
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.96
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.14
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.06
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.03
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.33
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.71
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.18
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.80
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.36
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.21
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.81
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.59
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.56
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.07
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.93
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.