Gene detail

Detailed information of OS493_015980-T1 in Lophelia pertusa

Genomic Location: scaffold_48:2269683...2274264
NR annotation: KAJ7333887.1, hypothetical protein OS493_015980 [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
Q8T2K9	Malate synthase OS=Dictyostelium discoideum OX=44689 GN=masA PE=2 SV=2
P28344	Malate synthase, glyoxysomal OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) OX=227321 GN=acuE PE=3 SV=3

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
PF01274 all species →	MS_TIM-barrel	Malate synthase, TIM barrel domain	Domain	Interproscan
PF20656 all species →	MS_N	Malate synthase, N-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006252 all species →	Family	Malate synthase A	Interproscan
IPR048355 all species →	Domain	Malate synthase, C-terminal domain	Interproscan
IPR001465 all species →	Domain	Malate synthase, TIM barrel domain	Interproscan
IPR046363 all species →	Homologous_superfamily	Malate synthase, N-terminal and TIM-barrel domains	Interproscan
IPR011076 all species →	Homologous_superfamily	Malate synthase superfamily	Interproscan
IPR048356 all species →	Domain	Malate synthase, N-terminal domain	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:0004474 all species →	Molecular Function	malate synthase activity	Interproscan
GO:0006097 all species →	Biological Process	glyoxylate cycle	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005782 all species →	Cellular Component	peroxisomal matrix	Interproscan
GO:0003824 all species →	Molecular Function	catalytic 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
K01638	aceB, glcB; malate synthase	EC:2.3.3.9	Glyoxylate and dicarboxylate metabolism	ko00630	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_015980-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

110TPM > 0

7Conditions

748.5Max TPM

124.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	35.16	48.34
polyp at pH7 6	18	18	44.08	61.88
coral polyp · control treatment	16	16	114.36	396.76
coral polyp · oil and dispersant treatment	16	16	272.97	569.70
coral polyp · oil treatment	16	16	111.62	263.18
coral polyp · dispersant treatment	16	16	241.55	748.49
Polyp	10	10	37.64	56.08

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.34
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.68
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.39
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.68
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.94
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.79
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.46
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.19
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.25
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.64
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.71
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.09
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.26
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.63
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.16
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.59
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.62
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.88
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.88
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.65
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.44
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.61
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.46
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.32
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.30
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.56
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.41
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.54
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.98
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.20
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.73
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.19
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.72
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.80
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	396.76
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	256.80
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	141.67
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	135.53
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	133.36
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	98.19
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.29
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.16
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.95
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.16
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.86
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.91
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.49
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.38
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.59
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.71
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	569.70
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	438.41
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	416.78
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	386.23
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	369.29
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	355.16
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	326.44
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	263.87
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	254.99
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	178.15
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	174.30
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	157.48
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	150.17
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	136.14
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	121.19
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.20
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	263.18
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	169.33
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.52
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	130.75
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	125.33
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.64
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	121.11
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.81
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	95.52
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	94.49
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	87.78
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	74.54
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.96
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.45
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.13
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.41
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	748.49
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	445.09
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	392.14
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	285.35
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	255.75
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	242.32
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	216.03
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	200.98
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	174.03
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	168.60
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	161.80
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	133.39
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	125.44
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	119.17
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	114.71
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.55
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	56.08
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	55.92
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	48.34
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	39.31
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	37.34
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	36.55
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	32.99
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	32.19
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	20.37
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	17.33

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.