Gene detail

Detailed information of OS493_024648-T1 in Lophelia pertusa

Genomic Location: scaffold_116:405778...415204
NR annotation: KAJ7383959.1, DNA-directed RNA polymerase III subunit RPC6 [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
Q2T9S3	DNA-directed RNA polymerase III subunit RPC6 OS=Bos taurus OX=9913 GN=POLR3F PE=2 SV=1
Q9H1D9	DNA-directed RNA polymerase III subunit RPC6 OS=Homo sapiens OX=9606 GN=POLR3F PE=1 SV=1
Q921X6	DNA-directed RNA polymerase III subunit RPC6 OS=Mus musculus OX=10090 GN=Polr3f PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007483 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05158 all species →	RNA_pol_Rpc34	RNA polymerase Rpc34 subunit	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007832 all species →	Family	RNA polymerase Rpc34	Interproscan
IPR016049 all species →	Family	RNA polymerase Rpc34-like	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12780 all species →	RNA POLYMERASE III DNA DIRECTED , 39KD SUBUNIT-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005666 all species →	Cellular Component	RNA polymerase III complex	Interproscan
GO:0006383 all species →	Biological Process	transcription by RNA polymerase III	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
K03025	RPC6, POLR3F; DNA-directed RNA polymerase III subunit RPC6	-	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_024648-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

12.1Max TPM

5.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	4.76	8.64
polyp at pH7 6	18	16	5.95	8.28
coral polyp · control treatment	16	16	7.01	12.15
coral polyp · oil and dispersant treatment	16	16	5.17	11.60
coral polyp · oil treatment	16	16	6.36	11.02
coral polyp · dispersant treatment	16	16	4.14	11.33
Polyp	10	9	5.89	11.46

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.64
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.54
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.44
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.23
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.08
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.47
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.17
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.14
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.92
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.76
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.74
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.35
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.99
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.54
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.34
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.33
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.28
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.24
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.78
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.29
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.25
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.89
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.63
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.34
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.22
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.84
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.69
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.51
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.48
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.08
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	12.15
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.74
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.55
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.40
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.08
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.69
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.66
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.59
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.50
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.47
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.79
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.66
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.61
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.24
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.19
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.89
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.60
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.82
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.50
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.21
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.80
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.23
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.23
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.68
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.34
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.63
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.61
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.63
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.41
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.13
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.02
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.98
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.36
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.22
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.00
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.93
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.90
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.30
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.94
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.71
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.26
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.09
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.84
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.09
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.41
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.33
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.68
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.75
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.61
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.48
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.38
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.05
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.97
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.90
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.75
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.69
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.32
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.91
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.62
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.92
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.89
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	11.46
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	8.99
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.37
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	7.21
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	6.50
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.46
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.43
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.82
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.72
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.