Gene detail

Detailed information of OS493_019856-T1 in Lophelia pertusa

Genomic Location: scaffold_71:53854...62827
NR annotation: KAJ7358952.1, hypothetical protein OS493_019856 [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
Q13569	G/T mismatch-specific thymine DNA glycosylase OS=Homo sapiens OX=9606 GN=TDG PE=1 SV=2
P56581	G/T mismatch-specific thymine DNA glycosylase OS=Mus musculus OX=10090 GN=Tdg PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004290 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03167 all species →	UDG	Uracil DNA glycosylase superfamily	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015637 all species →	Family	Uracil DNA glycosylase family 2	Interproscan
IPR036895 all species →	Homologous_superfamily	Uracil-DNA glycosylase-like domain superfamily	Interproscan
IPR005122 all species →	Domain	Uracil-DNA glycosylase-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12159 all species →	G/T AND G/U MISMATCH-SPECIFIC DNA GLYCOSYLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000700 all species →	Molecular Function	mismatch base pair DNA N-glycosylase activity	Interproscan
GO:0004844 all species →	Molecular Function	uracil DNA N-glycosylase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006285 all species →	Biological Process	base-excision repair, AP site formation	Interproscan
GO:0008263 all species →	Molecular Function	pyrimidine-specific mismatch base pair DNA N-glycosylase 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
K20813	TDG; thymine-DNA glycosylase	EC:3.2.2.29	DNA repair and recombination proteins	ko03400	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_019856-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

22.8Max TPM

10.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.73	22.83
polyp at pH7 6	18	17	9.94	17.98
coral polyp · control treatment	16	16	11.37	18.31
coral polyp · oil and dispersant treatment	16	16	8.81	13.61
coral polyp · oil treatment	16	16	12.97	17.31
coral polyp · dispersant treatment	16	16	8.20	13.52
Polyp	10	10	10.58	20.58

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.83
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.93
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.16
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.14
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.33
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.13
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.71
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.67
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.43
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.41
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.78
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.70
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.65
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.47
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.78
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.86
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.72
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.44
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.98
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.86
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.19
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.85
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.59
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.17
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.27
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.10
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.03
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.88
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.49
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.90
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.69
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.27
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.49
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.31
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.33
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.58
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.35
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.90
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.16
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.07
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.97
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.77
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.20
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.71
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.65
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.67
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.38
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.15
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.77
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.61
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.60
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.65
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.71
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.72
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.97
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.80
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.72
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.65
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.19
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.14
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.52
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.37
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.36
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.31
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.33
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.21
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.13
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.40
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.39
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.81
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.00
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.61
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.52
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.13
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.14
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.69
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.52
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.41
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.30
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.69
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.55
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.35
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.31
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.41
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.03
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.67
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.46
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.37
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.76
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.92
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.52
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.95
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	20.58
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	16.85
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.86
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.74
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	9.57
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	9.35
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.32
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	6.40
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.01

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.