Gene detail

Detailed information of OS493_013290-T1 in Lophelia pertusa

Genomic Location: scaffold_35:2711945...2713644
NR annotation: KAJ7362193.1, hypothetical protein OS493_013290 [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
O35261	Transcription factor E2F3 OS=Mus musculus OX=10090 GN=E2f3 PE=1 SV=2
O00716	Transcription factor E2F3 OS=Homo sapiens OX=9606 GN=E2F3 PE=1 SV=1
P56931	Transcription factor E2F2 OS=Mus musculus OX=10090 GN=E2f2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001946 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02319 all species →	E2F_TDP	E2F/DP family winged-helix DNA-binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003316 all species →	Domain	E2F/DP family, winged-helix DNA-binding domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR037241 all species →	Homologous_superfamily	E2F-DP heterodimerization region	Interproscan
IPR015633 all species →	Family	E2F Family	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12081 all species →	TRANSCRIPTION FACTOR E2F	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0090575 all species →	Cellular Component	RNA polymerase II transcription regulator 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_013290-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_013290-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

83TPM > 0

7Conditions

12.2Max TPM

1.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	13	1.88	5.41
polyp at pH7 6	18	11	1.49	4.74
coral polyp · control treatment	16	14	1.93	12.25
coral polyp · oil and dispersant treatment	16	12	1.16	4.87
coral polyp · oil treatment	16	13	1.79	5.06
coral polyp · dispersant treatment	16	13	1.59	5.20
Polyp	10	7	1.44	4.10

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.41
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.04
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.94
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.73
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.67
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.62
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.56
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.48
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.03
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.96
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.90
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.81
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.64
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.74
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.39
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.35
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.04
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.24
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.14
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.63
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.40
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.23
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.20
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.52
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	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	12.25
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.67
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.38
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.25
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.84
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.59
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.44
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.31
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.08
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.02
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.84
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.78
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.30
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.16
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.87
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.29
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.49
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.49
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.39
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.13
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.73
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.70
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.38
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.30
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.06
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.40
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.68
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.62
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.05
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.47
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.21
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.16
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.99
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.83
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.40
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.39
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.20
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.15
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.97
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.01
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.71
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.53
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.44
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.52
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.31
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.23
SRR16705967	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
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.10
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.67
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.02
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.83
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.55
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.29
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.89
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	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.