Gene detail

Detailed information of OS493_003402-T1 in Lophelia pertusa

Genomic Location: scaffold_7:1012947...1014595
NR annotation: KAJ7393743.1, Mothers against decapentaplegic 7 [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
O35182	Mothers against decapentaplegic homolog 6 OS=Mus musculus OX=10090 GN=Smad6 PE=1 SV=1
O43541	Mothers against decapentaplegic homolog 6 OS=Homo sapiens OX=9606 GN=SMAD6 PE=1 SV=2
Q9W734	Mothers against decapentaplegic homolog 6 OS=Gallus gallus OX=9031 GN=SMAD6 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008144 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03165 all species →	MH1	MH1 domain	Domain	Interproscan
PF03166 all species →	MH2	MH2 domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013019 all species →	Domain	MAD homology, MH1	Interproscan
IPR001132 all species →	Domain	SMAD domain, Dwarfin-type	Interproscan
IPR003619 all species →	Domain	MAD homology 1, Dwarfin-type	Interproscan
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR036578 all species →	Homologous_superfamily	SMAD MH1 domain superfamily	Interproscan
IPR017855 all species →	Homologous_superfamily	SMAD-like domain superfamily	Interproscan
IPR013790 all species →	Family	Dwarfin	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13703 all species →	SMAD	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0007179 all species →	Biological Process	transforming growth factor beta receptor signaling pathway	Interproscan
GO:0009653 all species →	Biological Process	anatomical structure morphogenesis	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0060395 all species →	Biological Process	SMAD protein signal transduction	Interproscan
GO:0070411 all species →	Molecular Function	I-SMAD binding	Interproscan
GO:0071144 all species →	Cellular Component	heteromeric SMAD protein complex	Interproscan
GO:0140416 all species →	Molecular Function	transcription regulator inhibitor activity	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
K04677	SMAD6; mothers against decapentaplegic homolog 6	-	TGF-beta signaling pathway	ko04350	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_003402-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

110TPM > 0

7Conditions

195.9Max TPM

81.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	58.47	100.68
polyp at pH7 6	18	18	53.33	93.85
coral polyp · control treatment	16	16	76.42	130.01
coral polyp · oil and dispersant treatment	16	16	115.38	164.18
coral polyp · oil treatment	16	16	87.79	135.84
coral polyp · dispersant treatment	16	16	98.13	195.87
Polyp	10	10	84.87	167.93

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	100.68
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	87.93
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	70.39
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.94
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.94
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.79
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.75
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.69
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.38
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.73
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.28
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.00
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.42
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.47
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.83
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.56
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.40
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.27
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	93.85
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	93.41
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.52
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.91
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.74
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.22
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.52
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.62
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.05
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.64
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.23
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.17
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.72
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.44
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.06
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.71
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.42
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.69
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	130.01
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	98.50
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.27
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	89.48
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.18
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.51
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.41
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.55
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.23
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.06
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.18
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.50
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.39
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.19
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.04
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.31
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	164.18
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	151.32
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	150.77
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	134.20
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	131.74
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	131.25
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	129.75
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	127.59
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	125.35
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	120.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.08
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	109.06
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.34
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.90
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.75
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.79
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	135.84
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	114.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	111.88
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	109.43
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	100.54
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	98.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	93.21
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	88.76
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	87.30
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.53
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.33
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.08
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.09
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.72
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.82
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.01
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	195.87
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	124.65
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	121.13
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	107.37
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	104.78
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.19
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	99.72
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	97.60
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.99
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	85.52
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.76
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.31
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.66
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.25
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.47
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.89
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	167.93
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	136.03
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	101.40
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	95.31
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	73.10
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	65.04
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	59.80
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	50.73
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	50.15
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	49.26

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.