Gene detail

Detailed information of OS493_001158-T1 in Lophelia pertusa

Genomic Location: scaffold_2:5774484...5790035
NR annotation: KAJ7387813.1, Mediator of RNA polymerase II transcription subunit 23 [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
Q6P423	Mediator of RNA polymerase II transcription subunit 23 OS=Xenopus laevis OX=8355 GN=med23 PE=2 SV=1
Q80YQ2	Mediator of RNA polymerase II transcription subunit 23 OS=Mus musculus OX=10090 GN=Med23 PE=1 SV=2
Q5EB59	Mediator of RNA polymerase II transcription subunit 23 OS=Rattus norvegicus OX=10116 GN=Med23 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003031 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11573 all species →	Med23	Mediator complex subunit 23	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR021629 all species →	Family	Mediator complex, subunit Med23	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12691 all species →	MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 23	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0010628 all species →	Biological Process	positive regulation of gene expression	Interproscan
GO:0016592 all species →	Cellular Component	mediator 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_001158-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_001158-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

104TPM > 0

7Conditions

39.9Max TPM

13.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.93	20.50
polyp at pH7 6	18	15	9.57	16.72
coral polyp · control treatment	16	16	18.79	37.52
coral polyp · oil and dispersant treatment	16	16	15.34	21.96
coral polyp · oil treatment	16	16	15.47	25.78
coral polyp · dispersant treatment	16	15	17.47	39.92
Polyp	10	8	4.79	11.08

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.50
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.18
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.84
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.35
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.20
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.81
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.63
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.13
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.00
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.09
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.95
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.79
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.41
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.16
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.05
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.22
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.17
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.72
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.57
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.05
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.42
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.94
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.32
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.20
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.09
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.70
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.69
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.51
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.48
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.75
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.49
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.32
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
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
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.52
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.36
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.41
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.69
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.25
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.59
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.36
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.98
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.32
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.37
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.83
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.58
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.98
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.65
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.02
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.81
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.96
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.72
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.27
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.88
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.77
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.92
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.65
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.09
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.03
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.82
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.46
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.87
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.69
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.31
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.53
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.47
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.78
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.30
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.14
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.24
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.03
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.64
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.87
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.71
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.35
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.95
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.68
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.67
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.55
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.84
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.06
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.63
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.92
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.24
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.42
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.28
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.67
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.21
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.09
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.03
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.33
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.29
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.85
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.61
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.98
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.74
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.85
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.08
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.38
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.80
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.22
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.54
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.04
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.03
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.85
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.