Gene detail

Detailed information of OS493_001289-T1 in Lophelia pertusa

Genomic Location: scaffold_2:7794160...7796517
NR annotation: KAJ7387937.1, hypothetical protein OS493_001289 [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
Q9TXJ8	Putative ATP-dependent DNA helicase Q1 OS=Caenorhabditis elegans OX=6239 GN=K02F3.12 PE=3 SV=3
Q09811	ATP-dependent DNA helicase hus2/rqh1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=rqh1 PE=1 SV=1
O18017	RecQ-like DNA helicase blm-1 OS=Caenorhabditis elegans OX=6239 GN=him-6 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000285 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00270 all species →	DEAD	DEAD/DEAH box helicase	Domain	Interproscan
PF16124 all species →	RecQ_Zn_bind	RecQ zinc-binding	Domain	Interproscan
PF09382 all species →	RQC	RQC domain	Domain	Interproscan
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011545 all species →	Domain	DEAD/DEAH box helicase domain	Interproscan
IPR032284 all species →	Domain	ATP-dependent DNA helicase RecQ, zinc-binding domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR018982 all species →	Domain	RQC domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13710 all species →	DNA HELICASE RECQ FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0043138 all species →	Molecular Function	3'-5' DNA helicase activity	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
K10901	BLM, RECQL3, SGS1; bloom syndrome protein	EC:5.6.2.4	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_001289-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

93TPM > 0

7Conditions

7.7Max TPM

0.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	15	0.53	1.38
polyp at pH7 6	18	15	0.80	1.89
coral polyp · control treatment	16	14	1.29	7.70
coral polyp · oil and dispersant treatment	16	15	1.20	6.50
coral polyp · oil treatment	16	14	0.77	5.19
coral polyp · dispersant treatment	16	13	0.25	1.00
Polyp	10	7	0.23	0.48

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.38
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.19
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.85
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.77
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.74
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.73
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.66
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.61
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.59
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.57
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.42
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.17
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.17
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.13
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
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.89
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.78
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.70
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.58
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.52
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.46
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.07
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.77
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.74
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.50
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.49
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.47
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.15
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.15
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.14
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
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.70
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.62
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.03
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.95
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.46
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.57
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.45
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.43
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.32
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.29
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.25
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.24
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.24
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.09
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705972	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	6.50
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.05
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.34
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.96
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.64
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.42
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.33
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.26
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.25
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.24
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.18
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.08
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.05
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.19
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.79
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.56
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.59
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.54
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.44
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.43
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.40
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.36
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.26
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.26
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.21
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.15
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.12
SRR16705951	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
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.85
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.46
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.34
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.21
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.17
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.17
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.16
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.16
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.15
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.13
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.08
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.08
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
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.48
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.37
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.37
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.36
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.34
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.20
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.18
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.