Gene detail

Detailed information of OS493_015170-T1 in Lophelia pertusa

Genomic Location: scaffold_44:1668739...1672433
NR annotation: KAJ7385586.1, TATA box-binding protein-associated factor RNA polymerase I subunit B [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004741 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11781 all species →	zf-RRN7	Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR033599 all species →	Family	RNA polymerase I transcription initiation factor TAF1B/Rrn7	Interproscan
IPR021752 all species →	Domain	Transcription initiation factor Rrn7, Zinc-finger	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR31576 all species →	TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR RNA POLYMERASE I SUBUNIT B	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0001164 all species →	Molecular Function	RNA polymerase I core promoter sequence-specific DNA binding	Interproscan
GO:0001188 all species →	Biological Process	RNA polymerase I preinitiation complex assembly	Interproscan
GO:0005668 all species →	Cellular Component	RNA polymerase transcription factor SL1 complex	Interproscan
GO:0006360 all species →	Biological Process	transcription by RNA polymerase I	Interproscan
GO:0042790 all species →	Biological Process	nucleolar large rRNA transcription by RNA polymerase I	Interproscan
GO:0070860 all species →	Cellular Component	RNA polymerase I core factor 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_015170-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_015170-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

88TPM > 0

7Conditions

10.0Max TPM

1.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	11	1.29	3.07
polyp at pH7 6	18	12	1.24	2.84
coral polyp · control treatment	16	14	2.38	9.97
coral polyp · oil and dispersant treatment	16	15	1.39	3.26
coral polyp · oil treatment	16	16	1.64	3.86
coral polyp · dispersant treatment	16	14	1.72	4.18
Polyp	10	6	0.71	1.74

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.07
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.55
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.53
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.39
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.29
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.25
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.10
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.48
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.23
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.23
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
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	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
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.84
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.39
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.12
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.05
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.03
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.93
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.90
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.74
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.26
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.20
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.94
SRR11359500	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
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
SRR11359524	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	9.97
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.31
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.30
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.07
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.03
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.31
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.23
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.10
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.96
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.84
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.76
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.26
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.56
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.91
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.86
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.63
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.44
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.14
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.08
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.83
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.44
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.37
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.86
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.56
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.27
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.16
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.04
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.95
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.87
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.84
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.78
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.46
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.30
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.95
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.63
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.53
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.42
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.18
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.73
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.48
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.83
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.64
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.52
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.32
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.18
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.42
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.36
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.22
SRR16705953	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
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.74
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.55
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.30
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.02
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.86
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.67
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
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.