Gene detail

Detailed information of OS493_013179-T1 in Lophelia pertusa

Genomic Location: scaffold_35:931625...936351
NR annotation: KAJ7362088.1, GID complex subunit 4, VID24 [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
Q9CPY6	Glucose-induced degradation protein 4 homolog OS=Mus musculus OX=10090 GN=Gid4 PE=1 SV=1
Q8IVV7	Glucose-induced degradation protein 4 homolog OS=Homo sapiens OX=9606 GN=GID4 PE=1 SV=1
P38263	GID complex substrate-recognition subunit 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=VID24 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008920 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09783 all species →	Vac_ImportDeg	Vacuolar import and degradation protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018618 all species →	Family	Vacuolar import/degradation protein Vid24	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14534 all species →	VACUOLAR IMPORT AND DEGRADATION PROTEIN 24	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006623 all species →	Biological Process	protein targeting to vacuole	Interproscan
GO:0007039 all species →	Biological Process	protein catabolic process in the vacuole	Interproscan
GO:0034657 all species →	Cellular Component	GID complex	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0045721 all species →	Biological Process	negative regulation of gluconeogenesis	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
K23335	GID4; glucose-induced degradation protein 4	-	Ubiquitin system	ko04121	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_013179-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

108TPM > 0

7Conditions

91.0Max TPM

18.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	8.87	17.97
polyp at pH7 6	18	17	10.21	19.84
coral polyp · control treatment	16	16	23.98	79.96
coral polyp · oil and dispersant treatment	16	16	30.28	91.05
coral polyp · oil treatment	16	16	17.50	28.51
coral polyp · dispersant treatment	16	16	25.33	49.25
Polyp	10	9	8.91	19.59

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	-	17.97
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.93
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.72
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.97
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.37
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.60
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.33
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.11
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.65
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.54
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.33
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.24
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.14
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.06
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.90
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.48
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.41
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.84
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.34
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.48
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.85
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.18
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.81
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.57
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.84
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.42
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.78
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.55
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.50
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.48
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.45
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.41
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.33
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.96
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.17
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.50
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.91
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.87
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.65
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.69
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.07
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.64
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.56
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.40
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.73
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.94
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.71
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.70
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.21
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.05
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.66
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.33
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.98
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.99
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.89
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.07
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.13
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.92
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.07
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.28
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.09
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.40
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.27
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.04
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.51
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.55
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.15
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.33
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.98
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.22
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.12
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.70
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.34
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.26
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.60
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.91
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.70
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.17
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.90
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.25
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.31
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.09
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.85
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.30
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.51
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.56
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.54
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.45
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.19
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.60
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.09
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.45
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	19.59
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	12.83
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.96
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	10.98
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	10.12
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	8.01
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.14
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.69
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.77
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.