Gene detail

Detailed information of OS493_031287-T1 in Lophelia pertusa

Genomic Location: scaffold_213:517337...521550
NR annotation: KAJ7377014.1, General transcription factor IIF subunit 2 [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
Q8R0A0	General transcription factor IIF subunit 2 OS=Mus musculus OX=10090 GN=Gtf2f2 PE=1 SV=1
Q01750	General transcription factor IIF subunit 2 OS=Rattus norvegicus OX=10116 GN=Gtf2f2 PE=1 SV=1
Q2T9L9	General transcription factor IIF subunit 2 OS=Bos taurus OX=9913 GN=GTF2F2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004928 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17683 all species →	TFIIF_beta_N	TFIIF, beta subunit N-terminus	Family	Interproscan
PF02270 all species →	TFIIF_beta	TFIIF, beta subunit HTH domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
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
IPR040504 all species →	Domain	TFIIF, beta subunit, N-terminal	Interproscan
IPR011039 all species →	Homologous_superfamily	Transcription Factor IIF, Rap30/Rap74, interaction	Interproscan
IPR003196 all species →	Family	Transcription initiation factor IIF, beta subunit	Interproscan
IPR040450 all species →	Domain	TFIIF beta subunit, HTH domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10445 all species →	GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006367 all species →	Biological Process	transcription initiation at RNA polymerase II promoter	Interproscan
GO:0005674 all species →	Cellular Component	transcription factor TFIIF complex	Interproscan
GO:0006366 all species →	Biological Process	transcription by RNA polymerase II	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
K03139	TFIIF2, GTF2F2, TFG2; transcription initiation factor TFIIF subunit beta	EC:5.6.2.-	Transcription machinery	ko03021	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_031287-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

110TPM > 0

7Conditions

67.3Max TPM

28.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	26.82	35.95
polyp at pH7 6	18	18	27.72	45.36
coral polyp · control treatment	16	16	35.33	62.61
coral polyp · oil and dispersant treatment	16	16	26.81	39.30
coral polyp · oil treatment	16	16	29.51	41.38
coral polyp · dispersant treatment	16	16	19.88	33.12
Polyp	10	10	32.94	67.29

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.95
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.67
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.31
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.05
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.48
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.26
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.98
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.78
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.06
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.12
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.88
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.83
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.45
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.12
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.03
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.30
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.14
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.36
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.10
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.75
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.69
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.73
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.73
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.11
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.28
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.60
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.42
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.11
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.22
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.58
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.21
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.13
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.15
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	62.61
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.73
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.92
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.29
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.14
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.10
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.25
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.86
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.84
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.54
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.26
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.10
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.07
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.71
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.09
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.84
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.30
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.72
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.59
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.86
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.70
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.66
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.72
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.62
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.89
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.73
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.50
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.56
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.28
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.41
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.11
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.25
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.38
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.65
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.26
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.22
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.20
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.72
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.44
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.14
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.05
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.41
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.27
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.12
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.28
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.09
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.57
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.12
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.69
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.52
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.53
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.47
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.40
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.37
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.10
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.41
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.14
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.69
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.67
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.27
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.35
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.50
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.92
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	67.29
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	43.46
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	40.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	35.01
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	29.83
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	29.08
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	25.87
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	25.86
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	20.22
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.80

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.