Gene detail

Detailed information of OS493_037209-T1 in Lophelia pertusa

Genomic Location: scaffold_407:166534...170537
NR annotation: KAJ7351027.1, hypothetical protein OS493_037209 [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
G3MZY8	DNA-directed RNA polymerase II subunit RPB1 OS=Bos taurus OX=9913 GN=POLR2A PE=1 SV=2
P11414	DNA-directed RNA polymerase II subunit RPB1 OS=Cricetulus griseus OX=10029 GN=POLR2A PE=1 SV=2
P24928	DNA-directed RNA polymerase II subunit RPB1 OS=Homo sapiens OX=9606 GN=POLR2A PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005025 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05001 all species →	RNA_pol_Rpb1_R	RNA polymerase Rpb1 C-terminal repeat	Repeat	Interproscan
PF04998 all species →	RNA_pol_Rpb1_5	RNA polymerase Rpb1, domain 5	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000684 all species →	Repeat	RNA polymerase II, heptapeptide repeat, eukaryotic	Interproscan
IPR045867 all species →	Family	DNA-directed RNA polymerase, subunit beta-prime	Interproscan
IPR007081 all species →	Domain	RNA polymerase Rpb1, domain 5	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19376 all species →	DNA-DIRECTED RNA POLYMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006366 all species →	Biological Process	transcription by RNA polymerase II	Interproscan
GO:0001055 all species →	Molecular Function	RNA polymerase II activity	Interproscan
GO:0003899 all species →	Molecular Function	DNA-directed 5'-3' RNA polymerase activity	Interproscan
GO:0005665 all species →	Cellular Component	RNA polymerase II, core complex	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	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_037209-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_037209-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

86.0Max TPM

27.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	25.65	49.40
polyp at pH7 6	18	18	23.17	35.74
coral polyp · control treatment	16	16	30.46	66.76
coral polyp · oil and dispersant treatment	16	16	39.67	85.98
coral polyp · oil treatment	16	16	22.77	49.85
coral polyp · dispersant treatment	16	16	31.10	52.97
Polyp	10	10	15.15	29.03

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.40
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.88
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.53
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.67
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.61
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.04
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.42
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.24
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.69
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.90
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.61
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.07
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.09
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.98
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.01
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.16
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.63
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.83
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.99
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.75
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.21
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.89
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.54
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.82
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.98
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.43
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.22
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.17
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.65
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.06
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.27
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.88
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.69
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.76
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.46
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.70
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.53
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.24
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.47
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.63
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.23
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.05
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.79
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.71
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.13
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.71
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.27
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.75
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.02
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	85.98
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	61.14
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.63
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.49
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.33
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.26
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.38
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.38
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.77
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.71
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.66
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.77
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.45
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.03
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.96
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.85
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.62
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.30
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.16
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.05
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.50
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.61
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.94
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.35
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.36
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.49
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.61
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.17
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.84
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.88
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.57
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.97
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.89
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.23
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.95
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.09
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.78
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.39
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.08
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.19
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.47
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.64
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.21
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.59
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.60
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	29.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	23.60
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	22.75
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	21.74
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	17.04
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	16.25
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.06
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.83
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.06

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.