Gene detail

Detailed information of OS493_004280-T1 in Lophelia pertusa

Genomic Location: scaffold_8:4500109...4504383
NR annotation: KAJ7387299.1, Short transient receptor putative channel 2-like [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
Q6ZNB5	Protein XNDC1N OS=Homo sapiens OX=9606 GN=XNDC1N PE=2 SV=2
P18887	DNA repair protein XRCC1 OS=Homo sapiens OX=9606 GN=XRCC1 PE=1 SV=3
Q9ESZ0	DNA repair protein XRCC1 OS=Rattus norvegicus OX=10116 GN=Xrcc1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001841 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01834 all species →	XRCC1_N	XRCC1 N terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002706 all species →	Domain	DNA-repair protein Xrcc1, N-terminal	Interproscan
IPR008979 all species →	Homologous_superfamily	Galactose-binding-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11370 all species →	DNA-REPAIR PROTEIN XRCC1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006284 all species →	Biological Process	base-excision repair	Interproscan
GO:0000012 all species →	Biological Process	single strand break repair	Interproscan
GO:0003684 all species →	Molecular Function	damaged DNA binding	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_004280-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_004280-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

59TPM > 0

7Conditions

36.9Max TPM

1.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	7	0.39	1.99
polyp at pH7 6	18	6	0.41	1.92
coral polyp · control treatment	16	11	2.81	36.89
coral polyp · oil and dispersant treatment	16	9	2.52	35.19
coral polyp · oil treatment	16	9	0.39	1.66
coral polyp · dispersant treatment	16	12	0.88	2.39
Polyp	10	5	0.48	2.08

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.99
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.51
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.27
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.84
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.59
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.58
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.31
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
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
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359509	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
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.92
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.46
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.38
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.16
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.82
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.70
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.89
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.32
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.12
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.01
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.90
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.85
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.72
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.68
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.60
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.47
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.35
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.19
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.29
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.04
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.87
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.76
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.41
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.31
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.23
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.66
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.57
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.56
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.48
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.44
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.44
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.44
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.34
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.23
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.39
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.90
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.40
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.38
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.32
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.14
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.11
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.03
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.96
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.86
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.38
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.19
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.08
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.36
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.65
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.41
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
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.