Gene detail

Detailed information of OS493_027725-T1 in Lophelia pertusa

Genomic Location: scaffold_153:334856...343410
NR annotation: KAJ7377647.1, GRAM domain-containing protein 4 [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
Q6IC98	GRAM domain-containing protein 4 OS=Homo sapiens OX=9606 GN=GRAMD4 PE=1 SV=1
Q8CB44	GRAM domain-containing protein 4 OS=Mus musculus OX=10090 GN=Gramd4 PE=1 SV=1
A2RV80	GRAM domain-containing protein 4 OS=Xenopus laevis OX=8355 GN=gramd4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002180 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_027725-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR037847 all species →	Family	GRAM domain-containing protein 4	Interproscan
IPR011993 all species →	Homologous_superfamily	PH-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR37402 all species →	GRAM DOMAIN-CONTAINING PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006915 all species →	Biological Process	apoptotic process	Interproscan
GO:0034164 all species →	Biological Process	negative regulation of toll-like receptor 9 signaling pathway	Interproscan
GO:0043280 all species →	Biological Process	obsolete positive regulation of cysteine-type endopeptidase activity involved in apoptotic 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K23554	GRAMD4; GRAM domain-containing protein 4	-	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_027725-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

23.7Max TPM

9.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	6.93	12.70
polyp at pH7 6	18	18	6.97	10.46
coral polyp · control treatment	16	16	9.70	17.05
coral polyp · oil and dispersant treatment	16	16	14.87	22.09
coral polyp · oil treatment	16	16	9.55	17.16
coral polyp · dispersant treatment	16	16	12.92	23.73
Polyp	10	9	6.02	15.41

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.70
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.87
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.31
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.69
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.69
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.13
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.93
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.14
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.11
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.99
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.77
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.53
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.52
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.29
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.66
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.46
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.10
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.70
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.67
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.42
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.85
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.52
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.16
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.68
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.62
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.85
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.50
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.14
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.05
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.63
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.38
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.64
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.05
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.54
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.03
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.82
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.16
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.81
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.66
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.33
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.71
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.50
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.24
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.22
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.17
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.07
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.68
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.09
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.88
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.62
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.58
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.34
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.73
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.78
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.76
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.70
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.10
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.66
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.49
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.71
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.56
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.86
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.16
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.77
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.01
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.24
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.99
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.73
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.56
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.50
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.46
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.43
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.24
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.65
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.45
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.93
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.41
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.23
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.73
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.60
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.90
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.64
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.17
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.12
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.01
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.90
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.76
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.68
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.50
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.68
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.04
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.68
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	15.41
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.30
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.52
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.28
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.48
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.83
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.82
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.11
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.47
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.