Gene detail

Detailed information of OS493_040250-T1 in Lophelia pertusa

Genomic Location: scaffold_1942:6417...8823
NR annotation: KAJ7369254.1, mediator complex subunit Srb9 [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
A2VCZ5	Mediator of RNA polymerase II transcription subunit 13-like OS=Danio rerio OX=7955 GN=zgc:153454 PE=2 SV=1
Q5SWW4	Mediator of RNA polymerase II transcription subunit 13 OS=Mus musculus OX=10090 GN=Med13 PE=1 SV=1
Q9UHV7	Mediator of RNA polymerase II transcription subunit 13 OS=Homo sapiens OX=9606 GN=MED13 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003809 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06333 all species →	Med13_C	Mediator complex subunit 13 C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051139 all species →	Family	Mediator complex subunit 13	Interproscan
IPR009401 all species →	Domain	Mediator complex subunit Med13, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48249 all species →	MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 13	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003713 all species →	Molecular Function	transcription coactivator activity	Interproscan
GO:0016592 all species →	Cellular Component	mediator complex	Interproscan
GO:0045944 all species →	Biological Process	positive regulation of transcription by RNA polymerase II	Interproscan
GO:0003712 all species →	Molecular Function	transcription coregulator activity	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	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_040250-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_040250-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

95TPM > 0

7Conditions

9.7Max TPM

1.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.27	9.67
polyp at pH7 6	18	15	3.43	7.90
coral polyp · control treatment	16	15	1.25	2.80
coral polyp · oil and dispersant treatment	16	14	0.93	1.87
coral polyp · oil treatment	16	13	0.83	1.66
coral polyp · dispersant treatment	16	12	0.91	2.49
Polyp	10	8	0.88	1.82

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	-	9.67
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.92
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.55
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.18
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.41
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.99
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.95
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.45
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.07
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.96
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.62
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.56
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.64
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.52
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.52
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.03
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.58
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.17
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.90
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.36
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.79
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.55
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.94
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.64
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.34
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.18
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.14
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.97
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.96
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.23
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.84
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.65
SRR11359512	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
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.80
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.44
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.91
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.90
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.58
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.57
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.06
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.06
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.01
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.58
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.51
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.40
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.87
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.77
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.37
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.13
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.10
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.03
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.00
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.92
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.89
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.89
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.87
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.79
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.31
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.66
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.40
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.37
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.29
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.29
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.15
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.94
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.88
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.87
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.73
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.62
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.20
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.49
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.42
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.35
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.35
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.31
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.16
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.01
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.83
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.70
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.69
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.64
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.82
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.65
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.38
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.02
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.80
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.64
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.54
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.