Gene detail

Detailed information of OS493_004081-T1 in Lophelia pertusa

Genomic Location: scaffold_8:2097850...2111108
NR annotation: KAJ7387116.1, Mediator of RNA polymerase II transcription subunit 16 [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
Q566H4	Mediator of RNA polymerase II transcription subunit 16 OS=Xenopus laevis OX=8355 GN=med16 PE=2 SV=1
Q08D69	Mediator of RNA polymerase II transcription subunit 16 OS=Xenopus tropicalis OX=8364 GN=med16 PE=2 SV=1
Q9Y2X0	Mediator of RNA polymerase II transcription subunit 16 OS=Homo sapiens OX=9606 GN=MED16 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004824 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF20718 all species →	Med16_bridge	Mediator complex subunit 16, central helical bridge	Domain	Interproscan
PF11635 all species →	Med16_N	Mediator complex subunit 16, N-terminal	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR048338 all species →	Family	Mediator complex, subunit Med16	Interproscan
IPR048616 all species →	Domain	Mediator of RNA polymerase II transcription subunit 16 , central helical bridge	Interproscan
IPR021665 all species →	Domain	Mediator complex, subunit Med16, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13224 all species →	THYROID HORMONE RECEPTOR-ASSOCIATED PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016592 all species →	Cellular Component	mediator complex	Interproscan
GO:0045893 all species →	Biological Process	positive regulation of DNA-templated transcription	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_004081-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_004081-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

49.1Max TPM

14.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.52	18.76
polyp at pH7 6	18	18	13.80	17.99
coral polyp · control treatment	16	16	18.98	41.46
coral polyp · oil and dispersant treatment	16	16	17.97	49.09
coral polyp · oil treatment	16	16	15.55	28.59
coral polyp · dispersant treatment	16	16	11.90	24.07
Polyp	10	9	9.34	13.43

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.76
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.75
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.57
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.92
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.65
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.96
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.41
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.79
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.72
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.62
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.16
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.66
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.58
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.24
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.22
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.02
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.55
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.72
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.99
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.64
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.36
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.55
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.52
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.77
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.36
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.20
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.91
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.47
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.41
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.75
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.49
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.33
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.06
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.84
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.23
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.46
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.62
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.79
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.96
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.96
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.80
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.87
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.39
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.20
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.05
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.01
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.02
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.28
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.48
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.43
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.09
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.25
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.48
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.76
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.60
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.97
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.32
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.45
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.91
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.60
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.98
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.85
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.71
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.61
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.39
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.56
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.59
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.10
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.25
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.65
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.96
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.53
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.51
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.62
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.60
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.41
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.20
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.95
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.22
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.82
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.07
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.14
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.32
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.05
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.03
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.02
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.81
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.67
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.67
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.55
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.88
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.81
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.81
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.43
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	13.16
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.83
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	11.20
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.23
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.95
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.41
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.12
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.06
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.