Gene detail

Detailed information of OS493_037212-T1 in Lophelia pertusa

Genomic Location: scaffold_407:182178...184334
NR annotation: KAJ7351030.1, hypothetical protein OS493_037212 [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
PF04997 all species →	RNA_pol_Rpb1_1	RNA polymerase Rpb1, domain 1	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007080 all species →	Domain	RNA polymerase Rpb1, domain 1	Interproscan
IPR045867 all species →	Family	DNA-directed RNA polymerase, subunit beta-prime	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:0003899 all species →	Molecular Function	DNA-directed 5'-3' RNA polymerase activity	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	Interproscan
GO:0001055 all species →	Molecular Function	RNA polymerase II activity	Interproscan
GO:0005665 all species →	Cellular Component	RNA polymerase II, core 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_037212-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_037212-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

106TPM > 0

7Conditions

30.8Max TPM

8.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	5.08	9.69
polyp at pH7 6	18	16	5.33	10.38
coral polyp · control treatment	16	16	11.48	30.83
coral polyp · oil and dispersant treatment	16	16	13.03	29.39
coral polyp · oil treatment	16	16	8.07	18.42
coral polyp · dispersant treatment	16	16	11.82	18.34
Polyp	10	9	4.66	9.41

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	-	9.69
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.18
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.93
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.91
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.81
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.51
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.41
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.34
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.15
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.80
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.72
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.45
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.75
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.74
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.39
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.17
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.54
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.38
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.17
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.87
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.74
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.46
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.50
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.44
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.07
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.86
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.77
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.66
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.30
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.02
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.95
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.10
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.64
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	30.83
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.08
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.07
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.36
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.35
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.09
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.56
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.33
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.83
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.24
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.78
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.56
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.81
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.80
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.94
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.39
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.30
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.57
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.55
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.12
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.54
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.29
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.70
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.65
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.00
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.00
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.11
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.40
SRR16705947	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	4.53
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.61
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.54
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.90
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.35
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.93
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.60
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.87
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.82
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.75
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.38
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.33
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.96
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.93
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.48
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.34
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.53
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.07
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.77
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.75
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.76
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.57
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.79
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.71
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.78
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.70
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.42
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.70
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.08
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.41
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	6.53
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.26
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.20
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.82
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	4.82
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.75
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.