Gene detail

Detailed information of OS493_005854-T1 in Lophelia pertusa

Genomic Location: scaffold_12:1770397...1778072
NR annotation: KAJ7339456.1, Transcription initiation factor IIB [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
P29054	Transcription initiation factor IIB OS=Xenopus laevis OX=8355 GN=gtf2b PE=2 SV=1
P62915	Transcription initiation factor IIB OS=Mus musculus OX=10090 GN=Gtf2b PE=1 SV=1
P62916	Transcription initiation factor IIB OS=Rattus norvegicus OX=10116 GN=Gtf2b PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006822 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08271 all species →	TF_Zn_Ribbon	TFIIB zinc-binding	Domain	Interproscan
PF00382 all species →	TFIIB	Transcription factor TFIIB repeat	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013137 all species →	Domain	Zinc finger, TFIIB-type	Interproscan
IPR023486 all species →	Conserved_site	Transcription factor TFIIB, conserved site	Interproscan
IPR036915 all species →	Homologous_superfamily	Cyclin-like superfamily	Interproscan
IPR000812 all species →	Family	Transcription factor TFIIB	Interproscan
IPR013763 all species →	Domain	Cyclin-like domain	Interproscan
IPR013150 all species →	Domain	Transcription factor TFIIB, cyclin-like domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11618 all species →	TRANSCRIPTION INITIATION FACTOR IIB-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006352 all species →	Biological Process	DNA-templated transcription initiation	Interproscan
GO:0070897 all species →	Biological Process	transcription preinitiation complex assembly	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006367 all species →	Biological Process	transcription initiation at RNA polymerase II promoter	Interproscan
GO:0016251 all species →	Molecular Function	RNA polymerase II general transcription initiation factor activity	Interproscan
GO:0017025 all species →	Molecular Function	TBP-class protein binding	Interproscan
GO:0097550 all species →	Cellular Component	transcription preinitiation 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K03124	TFIIB, GTF2B, SUA7, tfb; transcription initiation factor TFIIB	-	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_005854-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

159.4Max TPM

29.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	12.66	19.61
polyp at pH7 6	18	18	12.92	17.14
coral polyp · control treatment	16	16	30.07	80.31
coral polyp · oil and dispersant treatment	16	16	53.44	100.24
coral polyp · oil treatment	16	16	23.73	38.01
coral polyp · dispersant treatment	16	16	60.94	159.37
Polyp	10	10	12.43	17.34

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	-	19.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.27
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.57
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.55
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.18
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.02
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.95
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.71
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.45
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.30
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.72
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.16
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.15
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.18
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.05
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.66
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.27
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.14
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.02
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.48
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.40
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.27
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.89
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.78
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.55
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.15
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.24
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.93
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.59
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.53
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.39
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.84
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.67
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.05
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.31
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.52
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.09
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.04
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.78
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.98
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.94
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.70
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.46
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.11
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.48
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.81
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.43
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.64
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.50
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	100.24
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	80.33
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	75.64
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.85
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.75
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.88
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.70
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.15
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.37
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.87
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.84
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.64
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.02
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.04
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.01
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.59
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.04
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.56
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.72
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.60
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.94
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.29
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.88
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.73
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.64
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.20
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.17
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.27
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.19
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.88
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	159.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.25
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.46
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	102.18
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	89.03
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.39
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.65
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.28
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.41
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.31
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.03
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.18
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.95
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.41
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.19
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.94
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.34
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	15.29
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.96
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	14.23
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	14.08
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	13.63
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	12.27
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.60
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.67
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.28

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.