Gene detail

Detailed information of OS493_000098-T1 in Lophelia pertusa

Genomic Location: scaffold_1:1104938...1105999
NR annotation: KAJ7394296.1, hypothetical protein OS493_000098 [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
Q9QXE2	DNA polymerase lambda OS=Mus musculus OX=10090 GN=Poll PE=2 SV=1
Q9UGP5	DNA polymerase lambda OS=Homo sapiens OX=9606 GN=POLL PE=1 SV=1
Q5RKI3	DNA polymerase lambda OS=Rattus norvegicus OX=10116 GN=Poll PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001983 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14716 all species →	HHH_8	Helix-hairpin-helix domain	Domain	Interproscan
PF00533 all species →	BRCT	BRCA1 C Terminus (BRCT) domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027421 all species →	Homologous_superfamily	DNA polymerase lambda lyase domain superfamily	Interproscan
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR010996 all species →	Domain	DNA polymerase beta-like, N-terminal domain	Interproscan
IPR001357 all species →	Domain	BRCT domain	Interproscan
IPR022312 all species →	Family	DNA polymerase family X	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11276 all species →	DNA POLYMERASE TYPE-X FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003887 all species →	Molecular Function	DNA-directed DNA polymerase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	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_000098-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_000098-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

3.7Max TPM

1.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	1.61	2.71
polyp at pH7 6	18	17	1.85	3.75
coral polyp · control treatment	16	16	2.34	3.56
coral polyp · oil and dispersant treatment	16	16	1.55	2.52
coral polyp · oil treatment	16	16	1.95	3.31
coral polyp · dispersant treatment	16	16	0.97	2.37
Polyp	10	9	0.69	1.46

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.71
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.27
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.20
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.11
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.06
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.00
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.79
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.75
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.59
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.55
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.46
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.36
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.31
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.12
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.01
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.97
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.91
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.72
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.75
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.17
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.76
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.48
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.44
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.37
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.13
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.12
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.95
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.88
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.54
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.32
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.28
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.19
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.50
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.56
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.41
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.68
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.62
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.52
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.51
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.49
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.37
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.13
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.10
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.03
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.80
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.76
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.64
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.78
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.52
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.49
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.32
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.95
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.79
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.68
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.67
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.66
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.59
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.35
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.23
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.18
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.16
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.02
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.67
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.54
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.31
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.13
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.86
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.82
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.51
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.50
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.27
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.02
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.45
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.31
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.26
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.74
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.63
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.13
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.37
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.92
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.60
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.26
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.11
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.06
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.05
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.84
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.80
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.59
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.55
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.55
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.38
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.22
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.03
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.46
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.90
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.84
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.78
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.57
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.43
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.42
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.18
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.