Gene detail

Detailed information of OS493_026942-T1 in Lophelia pertusa

Genomic Location: scaffold_142:539345...551456
NR annotation: KAJ7371298.1, Non-ous end-joining factor 1 [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
Q6NV18	Non-homologous end-joining factor 1 OS=Danio rerio OX=7955 GN=nhej1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006260 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09302 all species →	XLF	XLF-Cernunnos, XRcc4-like factor, NHEJ component	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052287 all species →	Family	Non-homologous end-joining factor	Interproscan
IPR038051 all species →	Homologous_superfamily	XRCC4-like, N-terminal domain superfamily	Interproscan
IPR015381 all species →	Domain	XLF, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32235 all species →	NON-HOMOLOGOUS END-JOINING FACTOR 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0032807 all species →	Cellular Component	DNA ligase IV complex	Interproscan
GO:0045027 all species →	Molecular Function	DNA end binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	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
K10980	NHEJ1, XLF; non-homologous end-joining factor 1	-	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_026942-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

68.7Max TPM

11.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	14.00	29.85
polyp at pH7 6	18	18	13.34	34.45
coral polyp · control treatment	16	16	9.83	24.42
coral polyp · oil and dispersant treatment	16	16	5.79	12.12
coral polyp · oil treatment	16	16	11.22	21.52
coral polyp · dispersant treatment	16	16	6.49	25.91
Polyp	10	9	18.87	68.66

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.85
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.84
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.88
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.85
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.72
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.38
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.80
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.81
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.92
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.69
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.00
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.34
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.07
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.65
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.15
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.69
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.69
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.45
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.72
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.93
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.87
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.34
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.43
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.96
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.76
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.43
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.14
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.55
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.46
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.08
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.02
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.39
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.96
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.40
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.42
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.65
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.75
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.95
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.85
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.40
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.32
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.53
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.68
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.93
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.78
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.58
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.35
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.05
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.59
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.12
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.84
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.17
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.08
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.91
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.82
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.45
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.05
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.71
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.56
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.53
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.66
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.40
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.72
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.73
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.52
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.32
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.90
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.97
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.41
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.37
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.29
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.19
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.83
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.79
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.61
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.27
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.30
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.70
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.20
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.91
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.76
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.68
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.08
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.52
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.74
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.05
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.00
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.96
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.56
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.78
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.13
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.65
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.22
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	68.66
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	35.50
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	19.38
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	18.95
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	18.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	13.13
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.25
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.83
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.73
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.