Gene detail

Detailed information of OS493_004404-T1 in Lophelia pertusa

Genomic Location: scaffold_8:6186329...6191186
NR annotation: KAJ7387409.1, hypothetical protein OS493_004404 [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
Q9K9H0	Isocitrate lyase OS=Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) OX=272558 GN=aceA PE=3 SV=1
P51066	Isocitrate lyase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=aceA PE=3 SV=2
P0A5H4	Isocitrate lyase 1 OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) OX=233413 GN=icl PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002788 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00463 all species →	ICL	Isocitrate lyase family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018523 all species →	Conserved_site	Isocitrate lyase/phosphorylmutase, conserved site	Interproscan
IPR015813 all species →	Homologous_superfamily	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Interproscan
IPR039556 all species →	Domain	ICL/PEPM domain	Interproscan
IPR006254 all species →	Family	Isocitrate lyase	Interproscan
IPR040442 all species →	Homologous_superfamily	Pyruvate kinase-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21631 all species →	ISOCITRATE LYASE/MALATE SYNTHASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0004451 all species →	Molecular Function	isocitrate lyase activity	Interproscan
GO:0019752 all species →	Biological Process	carboxylic acid metabolic process	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
K01637	E4.1.3.1, aceA; isocitrate lyase	EC:4.1.3.1	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_004404-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

88TPM > 0

7Conditions

553.1Max TPM

46.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	7	0.51	2.06
polyp at pH7 6	18	10	1.87	7.29
coral polyp · control treatment	16	15	23.91	222.33
coral polyp · oil and dispersant treatment	16	16	133.90	553.10
coral polyp · oil treatment	16	15	13.05	34.86
coral polyp · dispersant treatment	16	16	140.57	389.53
Polyp	10	9	5.26	27.65

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	-	2.06
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.75
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.58
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.25
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.85
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.83
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.80
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
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
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359511	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
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.29
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.29
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.08
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.59
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.40
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.04
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.04
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.70
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.35
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
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359514	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
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	222.33
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.99
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.41
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.99
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.76
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.09
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.37
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.35
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.07
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.87
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.80
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.80
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.53
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.46
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	553.10
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	512.48
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	442.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	139.89
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	107.99
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.94
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.72
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.03
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.35
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.50
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.33
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.67
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.75
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.95
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.50
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.51
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.86
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.38
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.30
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.89
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.34
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.71
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.71
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.66
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.59
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.17
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.13
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.35
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.27
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.01
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.40
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	389.53
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	359.63
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	286.63
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	241.76
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	208.73
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	140.56
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	120.23
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	115.08
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	93.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.03
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	69.77
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.12
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.91
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.06
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.45
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.60
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	27.65
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	12.96
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.69
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.09
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.28
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.22
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.19
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.15
SRR23025712	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.