Gene detail

Detailed information of OS493_003378-T1 in Lophelia pertusa

Genomic Location: scaffold_7:821937...828430
NR annotation: KAJ7393719.1, RNA polymerase II proximal promoter sequence-specific DNA binding [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
A0A1L8H0H2	DNA-binding protein RFX7 OS=Xenopus laevis OX=8355 GN=rfx7.L PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006718 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18326 all species →	RFX5_N	RFX5 N-terminal domain	Domain	Interproscan

InterPro

No InterPro signature was detected for OS493_003378-T1. This gene does have a gene model — the search simply returned no hit.

PANTHER

No PANTHER signature was detected for OS493_003378-T1. This gene does have a gene model — the search simply returned no hit.

Gene Ontology

No Gene Ontology signature was detected for OS493_003378-T1. This gene does have a gene model — the search simply returned no hit.

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_003378-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_003378-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

102TPM > 0

7Conditions

15.4Max TPM

3.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	3.85	6.19
polyp at pH7 6	18	15	3.31	6.24
coral polyp · control treatment	16	16	4.65	10.21
coral polyp · oil and dispersant treatment	16	16	3.13	14.67
coral polyp · oil treatment	16	16	3.37	5.94
coral polyp · dispersant treatment	16	14	4.03	15.45
Polyp	10	9	3.04	7.00

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.19
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.79
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.76
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.52
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.88
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.72
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.41
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.39
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.83
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.53
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.42
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.34
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.20
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.89
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.24
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.16
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.12
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.61
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.46
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.31
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.12
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.64
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.47
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.95
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.87
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.79
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.72
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.56
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.50
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
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
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.21
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.00
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.99
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.80
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.53
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.48
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.03
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.97
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.97
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.58
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.66
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.64
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.56
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.39
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.67
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.59
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.46
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.24
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.23
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.10
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.07
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.44
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.41
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.95
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.72
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.58
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.34
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.34
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.94
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.70
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.04
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.42
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.95
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.92
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.42
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.40
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.34
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.13
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.05
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.37
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.04
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.87
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.20
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.45
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.24
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.31
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.93
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.37
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.25
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.95
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.91
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.80
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.65
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.73
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.33
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.43
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.94
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.92
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.64
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.34
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.16
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.07
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.89
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.