Gene detail

Detailed information of OS493_001355-T1 in Lophelia pertusa

Genomic Location: scaffold_3:182167...203560
NR annotation: KAJ7381239.1, hypothetical protein OS493_001355 [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
Q4W5Z4	DNA (cytosine-5)-methyltransferase 3A OS=Gallus gallus OX=9031 GN=DNMT3A PE=2 SV=1
O88508	DNA (cytosine-5)-methyltransferase 3A OS=Mus musculus OX=10090 GN=Dnmt3a PE=1 SV=2
Q1LZ53	DNA (cytosine-5)-methyltransferase 3A OS=Rattus norvegicus OX=10116 GN=Dnmt3a PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004545 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21255 all species →	ADDz_Dnmt3b	DNMT3, ADD PHD zinc finger	Domain	Interproscan
PF00855 all species →	PWWP	PWWP domain	Domain	Interproscan
PF17980 all species →	ADD_DNMT3	Cysteine rich ADD domain in DNMT3	Domain	Interproscan
PF00145 all species →	DNA_methylase	C-5 cytosine-specific DNA methylase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR049554 all species →	Domain	DNMT3, ADD domain, PHD zinc finger	Interproscan
IPR000313 all species →	Domain	PWWP domain	Interproscan
IPR018117 all species →	Active_site	DNA methylase, C-5 cytosine-specific, active site	Interproscan
IPR040552 all species →	Domain	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Interproscan
IPR025766 all species →	Domain	ADD domain	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan
IPR001525 all species →	Family	C-5 cytosine methyltransferase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23068 all species →	DNA CYTOSINE-5- -METHYLTRANSFERASE 3-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase 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

No KEGG orthology assignment for OS493_001355-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_001355-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

27.4Max TPM

10.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	12.53	17.18
polyp at pH7 6	18	18	12.06	19.10
coral polyp · control treatment	16	16	10.06	19.34
coral polyp · oil and dispersant treatment	16	16	7.22	27.41
coral polyp · oil treatment	16	16	9.69	18.81
coral polyp · dispersant treatment	16	16	10.62	18.41
Polyp	10	10	10.85	20.78

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	-	17.18
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.40
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.21
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.19
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.99
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.82
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.42
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.18
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.74
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.51
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.23
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.16
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.01
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.91
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.60
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.39
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.94
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.72
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.10
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.90
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.02
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.30
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.84
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.77
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.73
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.55
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.21
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.87
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.93
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.69
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.46
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.81
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.69
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.14
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.66
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.34
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.68
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.17
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.65
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.73
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.02
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.80
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.64
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.94
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.06
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.56
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.96
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.23
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.13
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.83
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.41
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.21
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.90
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.22
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.88
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.46
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.18
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.83
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.32
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.08
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.40
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.57
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.21
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.08
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.99
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.76
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.81
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.93
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.09
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.84
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.83
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.07
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.10
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.82
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.91
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.76
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.55
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.90
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.51
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.27
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.41
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.32
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.15
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.08
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.40
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.49
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.11
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.39
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.17
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.96
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.74
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.64
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.59
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.43
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.24
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.75
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	20.78
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.75
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.66
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.43
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.34
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.63
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	8.56
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.73
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	3.33
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.29

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.