Gene detail

Detailed information of OS493_007508-T1 in Lophelia pertusa

Genomic Location: scaffold_16:3138187...3142075
NR annotation: KAJ7374404.1, Nucleic acid dioxygenase alkbh1 [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
Q13686	Nucleic acid dioxygenase ALKBH1 OS=Homo sapiens OX=9606 GN=ALKBH1 PE=1 SV=2
P0CB42	Nucleic acid dioxygenase ALKBH1 OS=Mus musculus OX=10090 GN=Alkbh1 PE=1 SV=1
Q54N08	Alpha-ketoglutarate-dependent dioxygenase alkB OS=Dictyostelium discoideum OX=44689 GN=alkB PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003429 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13532 all species →	2OG-FeII_Oxy_2	2OG-Fe(II) oxygenase superfamily	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR037151 all species →	Homologous_superfamily	Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily	Interproscan
IPR027450 all species →	Domain	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	Interproscan
IPR004574 all species →	Family	Alkylated DNA repair protein AlkB	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16557 all species →	ALKYLATED DNA REPAIR PROTEIN ALKB-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008198 all species →	Molecular Function	ferrous iron binding	Interproscan
GO:0035513 all species →	Biological Process	oxidative RNA demethylation	Interproscan
GO:0035515 all species →	Molecular Function	oxidative RNA demethylase activity	Interproscan
GO:0035516 all species →	Molecular Function	broad specificity oxidative DNA demethylase activity	Interproscan
GO:0035552 all species →	Biological Process	obsolete oxidative single-stranded DNA demethylation	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_007508-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_007508-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

101TPM > 0

7Conditions

9.1Max TPM

2.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	13	1.84	4.45
polyp at pH7 6	18	16	2.55	9.07
coral polyp · control treatment	16	16	2.72	4.95
coral polyp · oil and dispersant treatment	16	16	1.48	8.57
coral polyp · oil treatment	16	16	2.31	4.33
coral polyp · dispersant treatment	16	14	1.06	3.03
Polyp	10	10	2.15	4.24

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.45
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.36
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.23
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.10
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.80
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.69
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.43
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.09
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.92
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.73
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.37
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.04
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.07
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.47
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.65
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.51
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.22
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.67
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.67
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.26
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.94
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.94
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.90
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.87
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.19
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.93
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.80
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.95
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.70
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.14
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.77
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.63
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.62
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.35
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.99
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.42
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.67
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.45
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.40
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.01
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.89
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.58
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.57
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.95
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.58
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.43
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.41
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.36
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.18
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.98
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.79
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.62
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.62
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.61
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.52
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.45
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.39
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.26
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.33
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.75
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.29
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.10
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.69
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.32
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.78
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.78
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.76
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.69
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.64
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.60
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.59
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.56
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.31
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.03
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.22
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.61
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.29
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.22
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.14
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.01
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.84
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.78
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.73
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.69
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.46
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.18
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	4.24
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	2.80
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.76
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.31
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.17
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.98
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.96
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.77
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.60

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.