Gene detail

Detailed information of OS493_015729-T1 in Lophelia pertusa

Genomic Location: scaffold_47:2279899...2286740
NR annotation: KAJ7360621.1, Transcription factor e2f4 [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
Q6DE14	Transcription factor E2F4 OS=Xenopus laevis OX=8355 GN=e2f4 PE=1 SV=1
Q8R0K9	Transcription factor E2F4 OS=Mus musculus OX=10090 GN=E2f4 PE=1 SV=1
Q15329	Transcription factor E2F5 OS=Homo sapiens OX=9606 GN=E2F5 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001904 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02319 all species →	E2F_TDP	E2F/DP family winged-helix DNA-binding domain	Domain	Interproscan
PF16421 all species →	E2F_CC-MB	E2F transcription factor CC-MB domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015633 all species →	Family	E2F Family	Interproscan
IPR003316 all species →	Domain	E2F/DP family, winged-helix DNA-binding domain	Interproscan
IPR037241 all species →	Homologous_superfamily	E2F-DP heterodimerization region	Interproscan
IPR032198 all species →	Domain	E2F transcription factor, CC-MB domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	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: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
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0046983 all species →	Molecular Function	protein dimerization activity	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
K04682	E2F4_5; transcription factor E2F4/5	-	Transcription factors	ko03000	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_015729-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

109.5Max TPM

14.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	15.84	21.39
polyp at pH7 6	18	18	16.41	24.23
coral polyp · control treatment	16	16	19.33	102.30
coral polyp · oil and dispersant treatment	16	16	14.97	109.49
coral polyp · oil treatment	16	16	15.30	26.40
coral polyp · dispersant treatment	16	15	8.93	22.55
Polyp	10	10	9.27	20.97

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.39
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.34
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.09
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.30
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.67
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.65
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.44
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.00
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.91
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.63
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.46
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.34
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.12
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.30
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.57
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.46
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.33
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.10
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.23
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.47
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.05
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.69
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.19
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.66
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.50
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.45
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.39
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.38
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.15
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.36
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.01
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.47
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.70
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.12
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	102.30
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.70
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.92
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.54
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.29
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.79
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.49
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.75
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.64
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.77
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.75
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.92
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.29
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.33
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	109.49
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.17
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.38
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.58
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.39
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.91
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.57
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.59
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.60
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.59
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.38
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.04
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.28
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.04
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.80
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.75
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.40
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.33
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.17
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.18
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.05
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.19
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.35
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.49
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.90
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.13
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.37
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.05
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.13
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.03
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.55
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.20
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.73
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.86
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.82
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.88
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.46
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.62
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.57
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.54
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.45
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.10
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.89
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.09
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.08
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	20.97
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	18.31
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.36
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	10.73
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.30
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.99
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.87
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.68
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.19

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.