Gene detail

Detailed information of OS493_023297-T1 in Lophelia pertusa

Genomic Location: scaffold_102:465035...473918
NR annotation: KAJ7329005.1, hypothetical protein OS493_023297 [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
Q6DFW0	Guanine nucleotide exchange factor C9orf72 homolog OS=Mus musculus OX=10090 GN=C9orf72 PE=1 SV=2
Q66HC3	Guanine nucleotide exchange factor C9orf72 homolog OS=Rattus norvegicus OX=10116 GN=C9orf72 PE=2 SV=1
Q96LT7	Guanine nucleotide exchange factor C9orf72 OS=Homo sapiens OX=9606 GN=C9orf72 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005942 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF15019 all species →	C9orf72-like	C9orf72-like protein family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027819 all species →	Family	Guanine nucleotide exchange factor C9orf72	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR31855 all species →	GUANINE NUCLEOTIDE EXCHANGE C9ORF72	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005768 all species →	Cellular Component	endosome	Interproscan
GO:0005776 all species →	Cellular Component	autophagosome	Interproscan
GO:0006897 all species →	Biological Process	endocytosis	Interproscan
GO:0006914 all species →	Biological Process	autophagy	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_023297-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_023297-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

24.6Max TPM

8.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	6.65	10.73
polyp at pH7 6	18	16	6.90	13.93
coral polyp · control treatment	16	16	13.20	24.60
coral polyp · oil and dispersant treatment	16	16	8.10	15.25
coral polyp · oil treatment	16	16	9.05	20.35
coral polyp · dispersant treatment	16	16	8.08	12.69
Polyp	10	10	5.39	12.21

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	-	10.73
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.65
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.83
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.22
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.60
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.30
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.83
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.71
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.53
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.95
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.65
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.61
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.46
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.38
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.37
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.28
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.83
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.70
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.93
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.13
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.34
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.31
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.19
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.94
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.88
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.87
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.82
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.74
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.69
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.07
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.36
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.27
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.47
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.13
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	24.60
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.12
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.80
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.63
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.57
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.26
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.19
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.10
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.77
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.23
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.22
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.33
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.75
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.94
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.77
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.93
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.25
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.03
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.10
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.58
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.93
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.51
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.45
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.34
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.49
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.46
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.23
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.72
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.79
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.54
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.87
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.35
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.57
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.78
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.15
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.14
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.38
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.21
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.62
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.62
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.40
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.92
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.64
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.75
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.58
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.96
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.69
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.36
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.91
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.90
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.87
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.60
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.81
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.89
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.49
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.16
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.05
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.72
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.63
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.34
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.83
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.21
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.18
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	5.90
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.64
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.50
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.16
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.68
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.43
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.35
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.86

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.