Gene detail

Detailed information of OS493_035449-T1 in Lophelia pertusa

Genomic Location: scaffold_321:55925...60617
NR annotation: KAJ7376309.1, hypothetical protein OS493_035449 [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
P95329	Malate synthase OS=Myxococcus xanthus (strain DK1622) OX=246197 GN=mls PE=3 SV=2
P13244	Malate synthase, glyoxysomal OS=Brassica napus OX=3708 PE=2 SV=1
Q9LZC3	Malate synthase OS=Arabidopsis thaliana OX=3702 GN=MLS PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002008 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF20659 all species →	MS_C	Malate synthase, C-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR048355 all species →	Domain	Malate synthase, C-terminal domain	Interproscan
IPR011076 all species →	Homologous_superfamily	Malate synthase superfamily	Interproscan
IPR046363 all species →	Homologous_superfamily	Malate synthase, N-terminal and TIM-barrel domains	Interproscan
IPR006252 all species →	Family	Malate synthase A	Interproscan
IPR044856 all species →	Homologous_superfamily	Malate synthase, C-terminal superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR42902 all species →	MALATE SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0004474 all species →	Molecular Function	malate synthase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006097 all species →	Biological Process	glyoxylate cycle	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_035449-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_035449-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

25.6Max TPM

5.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	8.08	18.06
polyp at pH7 6	18	18	8.23	25.56
coral polyp · control treatment	16	16	4.08	7.34
coral polyp · oil and dispersant treatment	16	16	3.28	10.80
coral polyp · oil treatment	16	16	4.93	11.33
coral polyp · dispersant treatment	16	16	2.95	5.40
Polyp	10	9	3.27	6.64

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.06
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.78
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.39
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.32
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.04
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.25
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.85
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.38
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.93
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.89
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.72
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.54
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.29
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.25
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.12
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.93
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.56
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.17
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.41
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.38
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.64
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.51
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.64
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.56
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.14
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.10
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.94
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.33
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.95
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.41
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.34
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.13
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.38
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.32
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.87
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.65
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.50
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.23
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.19
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.97
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.67
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.42
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.25
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.22
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.86
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.80
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.83
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.67
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.50
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.86
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.82
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.65
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.64
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.31
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.83
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.82
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.66
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.57
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.19
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.04
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.23
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.33
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.50
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.55
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.25
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.23
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.18
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.00
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.28
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.71
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.70
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.51
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.39
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.82
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.81
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.69
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.01
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.40
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.16
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.13
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.96
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.65
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.62
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.89
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.79
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.61
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.34
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.25
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.99
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.90
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.13
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.51
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.64
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.49
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	4.34
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.23
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	2.74
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.71
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.67
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.64
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.