Gene detail

Detailed information of OS493_004394-T1 in Lophelia pertusa

Genomic Location: scaffold_8:6008535...6018387
NR annotation: KAJ7387400.1, General transcription factor IIH subunit 3 [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
Q13889	General transcription factor IIH subunit 3 OS=Homo sapiens OX=9606 GN=GTF2H3 PE=1 SV=2
Q561R7	General transcription factor IIH subunit 3 OS=Rattus norvegicus OX=10116 GN=Gtf2h3 PE=2 SV=1
Q05B56	General transcription factor IIH subunit 3 OS=Bos taurus OX=9913 GN=GTF2H3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004525 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03850 all species →	Tfb4	Transcription factor Tfb4	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR004600 all species →	Family	TFIIH subunit Tfb4/GTF2H3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12831 all species →	TRANSCRIPTION INITIATION FACTOR IIH TFIIH , POLYPEPTIDE 3-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000439 all species →	Cellular Component	transcription factor TFIIH core complex	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0005675 all species →	Cellular Component	transcription factor TFIIH holo complex	Interproscan
GO:0070816 all species →	Biological Process	obsolete phosphorylation of RNA polymerase II C-terminal domain	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
K03143	TFIIH3, GTF2H3, TFB4; transcription initiation factor TFIIH subunit 3	-	DNA repair and recombination proteins	ko03400	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_004394-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

19.5Max TPM

6.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.97	13.92
polyp at pH7 6	18	18	9.06	16.90
coral polyp · control treatment	16	16	5.92	12.12
coral polyp · oil and dispersant treatment	16	16	4.49	17.90
coral polyp · oil treatment	16	16	5.77	10.51
coral polyp · dispersant treatment	16	16	3.65	6.38
Polyp	10	9	10.30	19.46

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	-	13.92
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.53
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.78
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.81
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.58
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.24
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.08
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.50
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.95
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.68
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.53
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.38
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.34
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.02
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.33
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.90
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.90
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.23
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.82
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.09
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.92
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.89
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.49
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.14
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.11
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.73
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.11
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.92
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.36
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.20
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.25
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.77
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.12
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.44
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.32
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.17
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.64
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.40
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.20
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.97
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.83
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.53
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.38
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.91
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.69
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.41
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.88
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.90
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.02
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.87
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.93
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.64
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.26
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.85
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.35
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.31
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.03
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.02
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.87
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.62
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.30
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.22
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.59
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.51
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.14
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.64
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.53
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.44
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.78
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.23
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.55
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.53
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.43
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.41
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.15
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.12
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.11
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.06
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.38
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.07
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.81
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.69
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.47
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.32
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.75
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.61
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.59
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.58
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.47
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.37
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	19.46
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	19.43
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.54
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.80
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.11
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	8.85
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.05
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.78
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.