Gene detail

Detailed information of OS493_006039-T1 in Lophelia pertusa

Genomic Location: scaffold_12:3905768...3908565
NR annotation: KAJ7339633.1, hypothetical protein OS493_006039 [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
Q64267	DNA repair protein complementing XP-A cells homolog OS=Mus musculus OX=10090 GN=Xpa PE=1 SV=2
P27088	DNA repair protein complementing XP-A cells homolog OS=Xenopus laevis OX=8355 GN=xpa PE=2 SV=1
P27089	DNA repair protein complementing XP-A cells homolog OS=Gallus gallus OX=9031 GN=XPA PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005117 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01286 all species →	XPA_N	XPA protein N-terminal	Domain	Interproscan
PF05181 all species →	XPA_C	XPA protein C-terminus	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000465 all species →	Family	XPA/RAD14	Interproscan
IPR022652 all species →	Conserved_site	Zinc finger, XPA-type, conserved site	Interproscan
IPR037129 all species →	Homologous_superfamily	XPA domain superfamily	Interproscan
IPR022656 all species →	Domain	XPA, C-terminal	Interproscan
IPR009061 all species →	Homologous_superfamily	Putative DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10142 all species →	DNA REPAIR PROTEIN COMPLEMENTING XP-A CELLS	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000110 all species →	Cellular Component	nucleotide-excision repair factor 1 complex	Interproscan
GO:0000715 all species →	Biological Process	nucleotide-excision repair, DNA damage recognition	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	Interproscan
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0033683 all species →	Biological Process	obsolete nucleotide-excision repair, DNA incision	Interproscan
GO:0070914 all species →	Biological Process	UV-damage excision repair	Interproscan
GO:1901255 all species →	Biological Process	nucleotide-excision repair involved in interstrand cross-link 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
K10847	XPA; DNA-repair protein complementing XP-A cells	-	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_006039-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

108TPM > 0

7Conditions

34.0Max TPM

6.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	6.22	9.12
polyp at pH7 6	18	18	7.07	13.40
coral polyp · control treatment	16	16	6.88	17.36
coral polyp · oil and dispersant treatment	16	16	5.69	33.96
coral polyp · oil treatment	16	16	6.16	8.41
coral polyp · dispersant treatment	16	16	3.16	7.67
Polyp	10	9	8.92	21.70

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.12
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.64
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.49
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.11
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.97
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.85
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.79
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.70
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.54
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.84
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.73
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.77
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.98
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.59
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.95
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.94
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.40
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.47
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.19
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.13
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.80
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.23
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.20
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.98
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.71
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.53
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.24
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.06
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.03
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.39
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.18
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.87
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.76
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.36
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.26
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.15
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.97
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.28
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.96
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.86
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.79
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.31
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.09
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.51
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.40
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.87
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.62
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.35
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.96
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.69
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.61
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.40
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.86
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.86
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.80
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.97
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.02
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.99
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.86
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.51
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.47
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.37
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.32
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.41
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.69
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.65
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.01
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.66
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.42
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.21
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.10
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.04
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.80
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.61
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.19
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.16
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.08
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.56
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.67
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.77
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.21
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.96
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.76
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.52
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.40
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.10
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.71
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.46
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.76
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.70
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.51
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.40
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	21.70
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	17.10
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.59
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.82
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.02
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.78
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	7.48
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.98
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.73
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.