Gene detail

Detailed information of OS493_005611-T1 in Lophelia pertusa

Genomic Location: scaffold_11:3143985...3147717
NR annotation: KAJ7365502.1, DNA-directed RNA polymerase II subunit RPB9 [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
P36954	DNA-directed RNA polymerase II subunit RPB9 OS=Homo sapiens OX=9606 GN=POLR2I PE=1 SV=1
P60898	DNA-directed RNA polymerase II subunit RPB9 OS=Mus musculus OX=10090 GN=Polr2i PE=1 SV=1
P60899	DNA-directed RNA polymerase II subunit RPB9 OS=Sus scrofa OX=9823 GN=POLR2I PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009375 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01096 all species →	TFIIS_C	Transcription factor S-II (TFIIS)	Domain	Interproscan
PF02150 all species →	RNA_POL_M_15KD	RNA polymerases M/15 Kd subunit	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001222 all species →	Domain	Zinc finger, TFIIS-type	Interproscan
IPR019761 all species →	Conserved_site	DNA-directed RNA polymerase M, 15kDa subunit, conserved site	Interproscan
IPR012164 all species →	Family	DNA-directed RNA polymerase subunit/transcription factor S	Interproscan
IPR034012 all species →	Domain	Pol II subunit B9, C-terminal zinc ribbon	Interproscan
IPR001529 all species →	Domain	DNA-directed RNA polymerase, M/15kDa subunit	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11239 all species →	DNA-DIRECTED RNA POLYMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003899 all species →	Molecular Function	DNA-directed 5'-3' RNA polymerase activity	Interproscan
GO:0001193 all species →	Biological Process	maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II	Interproscan
GO:0005665 all species →	Cellular Component	RNA polymerase II, core complex	Interproscan
GO:0006283 all species →	Biological Process	transcription-coupled nucleotide-excision repair	Interproscan
GO:0006367 all species →	Biological Process	transcription initiation at RNA polymerase II promoter	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
K03017	RPB9, POLR2I; DNA-directed RNA polymerase II subunit RPB9	-	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_005611-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

103TPM > 0

7Conditions

27.3Max TPM

10.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	13.03	20.66
polyp at pH7 6	18	15	12.71	21.69
coral polyp · control treatment	16	16	10.78	27.28
coral polyp · oil and dispersant treatment	16	15	7.45	16.06
coral polyp · oil treatment	16	16	11.66	16.55
coral polyp · dispersant treatment	16	15	6.11	12.01
Polyp	10	9	10.82	23.06

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	-	20.66
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.33
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.61
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.58
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.47
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.36
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.79
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.37
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.76
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.09
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.69
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.61
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.66
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.39
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.96
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.69
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.05
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.39
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.98
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.96
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.90
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.91
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.16
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.14
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.70
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.52
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.01
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.80
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.08
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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.28
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.57
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.39
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.86
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.99
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.42
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.56
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.41
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.98
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.34
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.68
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.60
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.48
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.19
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.93
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.27
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.47
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.11
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.36
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.36
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.75
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.92
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.47
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.96
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.19
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.12
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.98
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.22
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.04
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.55
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.05
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.38
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.10
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.03
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.42
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.05
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.78
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.86
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.06
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.86
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.35
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.94
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.23
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.14
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.70
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.01
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.64
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.54
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.83
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.63
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.26
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.62
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.42
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.61
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.42
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.58
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.91
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	23.06
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.03
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	13.29
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	12.19
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.67
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.31
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.95
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.58
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.08
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.