Gene detail

Detailed information of OS493_007573-T1 in Lophelia pertusa

Genomic Location: scaffold_16:3932357...3932695
NR annotation: KAJ7374467.1, Gem (Nuclear organelle) associated protein 6 [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009262 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06372 all species →	Gemin6	Gemin6 Sm-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR046857 all species →	Domain	Gem-associated protein 6, Sm-like domain	Interproscan
IPR009422 all species →	Family	Gem-associated protein 6	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14710 all species →	GEM-ASSOCIATED PROTEIN 6	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000245 all species →	Biological Process	spliceosomal complex assembly	Interproscan
GO:0000387 all species →	Biological Process	spliceosomal snRNP assembly	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_007573-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_007573-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

22.2Max TPM

3.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.97	13.08
polyp at pH7 6	18	18	4.28	7.80
coral polyp · control treatment	16	16	4.03	11.13
coral polyp · oil and dispersant treatment	16	16	3.61	22.21
coral polyp · oil treatment	16	16	3.74	8.06
coral polyp · dispersant treatment	16	15	2.42	5.65
Polyp	10	10	3.89	9.33

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.08
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.79
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.75
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.70
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.66
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.63
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.58
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.81
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.67
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.45
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.34
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.33
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.91
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.65
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.37
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.59
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.60
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.56
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.80
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.75
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.45
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.45
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.35
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.79
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.36
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.32
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.22
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.20
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.79
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.67
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.77
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.16
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.84
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.32
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.13
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.50
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.06
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.70
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.87
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.61
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.46
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.64
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.69
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.53
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.37
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.14
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.10
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.88
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.38
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.21
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.95
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.94
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.68
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.90
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.55
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.47
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.32
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.29
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.04
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.67
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.48
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.28
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.82
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.21
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.06
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.21
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.27
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.16
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.42
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.01
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.35
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.32
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.20
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.16
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.08
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.98
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.63
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.17
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.35
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.47
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.65
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.03
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.90
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.21
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.09
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.59
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.55
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.13
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.09
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.72
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.32
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.09
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.92
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.67
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.26
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.27
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.97
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.38
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.63
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.68
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.12
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.54

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.