Gene detail

Detailed information of OS493_003738-T1 in Lophelia pertusa

Genomic Location: scaffold_7:5433928...5447879
NR annotation: KAJ7394064.1, Mothers against decapentaplegic 4 [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
O70437	Mothers against decapentaplegic homolog 4 OS=Rattus norvegicus OX=10116 GN=Smad4 PE=1 SV=1
P97471	Mothers against decapentaplegic homolog 4 OS=Mus musculus OX=10090 GN=Smad4 PE=1 SV=2
Q13485	Mothers against decapentaplegic homolog 4 OS=Homo sapiens OX=9606 GN=SMAD4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006604 (this species only)

Pfam domain

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

InterPro

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

PANTHER

PANTHER term	Description	Source
PTHR13703 all species →	SMAD	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	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:0030509 all species →	Biological Process	BMP signaling pathway	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:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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
K04501	SMAD4; mothers against decapentaplegic homolog 4	-	AGE-RAGE signaling pathway in diabetic complications	ko04933	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_003738-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

38.2Max TPM

14.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.90	16.21
polyp at pH7 6	18	18	11.44	17.95
coral polyp · control treatment	16	16	21.07	35.67
coral polyp · oil and dispersant treatment	16	16	13.89	19.77
coral polyp · oil treatment	16	16	16.92	24.41
coral polyp · dispersant treatment	16	16	18.65	38.22
Polyp	10	10	6.85	12.87

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.21
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.46
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.19
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.59
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.41
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.72
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.27
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.27
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.21
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.78
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.64
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.53
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.50
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.08
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.43
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.74
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.90
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.28
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.95
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.73
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.22
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.45
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.42
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.50
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.43
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.03
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.09
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.09
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.52
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.54
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.54
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.30
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.39
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.15
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.67
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.85
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.84
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.71
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.19
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.66
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.00
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.93
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.03
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.69
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.53
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.31
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.23
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.12
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.86
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.45
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.77
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.35
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.80
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.49
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.31
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.29
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.50
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.20
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.73
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.61
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.58
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.97
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.02
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.98
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.63
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.97
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.41
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.45
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.45
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.30
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.85
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.01
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.94
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.85
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.76
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.35
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.47
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.86
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.56
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.24
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.18
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.22
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.69
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.19
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.41
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.15
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.38
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.16
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.67
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.30
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.97
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.93
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.60
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.35
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.87
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.48
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.37
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.12
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.57
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	6.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.83
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.64
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.22
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.08

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.