Gene detail

Detailed information of OS493_035577-T1 in Lophelia pertusa

Genomic Location: scaffold_325:154292...161870
NR annotation: KAJ7388793.1, DNA-directed RNA polymerase III subunit RPC3 [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
Q9BUI4	DNA-directed RNA polymerase III subunit RPC3 OS=Homo sapiens OX=9606 GN=POLR3C PE=1 SV=1
Q9D483	DNA-directed RNA polymerase III subunit RPC3 OS=Mus musculus OX=10090 GN=Polr3c PE=1 SV=1
Q5XIL3	DNA-directed RNA polymerase III subunit RPC3 OS=Rattus norvegicus OX=10116 GN=Polr3c PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005794 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05645 all species →	RNA_pol_Rpc82	RNA polymerase III subunit RPC82	Family	Interproscan
PF08221 all species →	HTH_9	RNA polymerase III subunit RPC82 helix-turn-helix domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008806 all species →	Domain	RNA polymerase III Rpc82, C -terminal	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR039748 all species →	Family	DNA-directed RNA polymerase III subunit RPC3	Interproscan
IPR013197 all species →	Domain	RNA polymerase III subunit RPC82-related, helix-turn-helix	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12949 all species →	RNA POLYMERASE III DNA DIRECTED -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	Interproscan
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005666 all species →	Cellular Component	RNA polymerase III 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_035577-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_035577-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

109TPM > 0

7Conditions

20.0Max TPM

4.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5.86	9.15
polyp at pH7 6	18	18	5.62	11.23
coral polyp · control treatment	16	16	6.33	18.74
coral polyp · oil and dispersant treatment	16	16	4.10	19.97
coral polyp · oil treatment	16	16	4.85	9.71
coral polyp · dispersant treatment	16	16	3.25	10.42
Polyp	10	9	3.83	9.53

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.15
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.84
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.29
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.27
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.85
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.80
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.29
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.97
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.97
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.67
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.27
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.92
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.64
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.25
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.11
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.34
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.18
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.70
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.23
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.30
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.27
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.18
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.03
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.89
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.85
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.69
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.67
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.55
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.38
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.04
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.54
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.51
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.24
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.91
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.26
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.66
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.74
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.36
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.50
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.13
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.78
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.77
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.96
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.03
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.58
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.26
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.95
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.88
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.26
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.99
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.08
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.97
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.80
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.35
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.14
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.05
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.51
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.06
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.87
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.83
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.56
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.43
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.28
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.07
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.80
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.71
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.59
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.55
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.12
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.93
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.44
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.57
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.24
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.62
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.53
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.12
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.88
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.78
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.66
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.42
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.42
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.59
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.28
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.14
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.32
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.69
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.47
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.28
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.25
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.23
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.06
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.05
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.92
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.92
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.25
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.09
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.53
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.81
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.17
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.91
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.83
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.64
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.38
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.55
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.51
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.