Gene detail

Detailed information of OS493_015981-T1 in Lophelia pertusa

Genomic Location: scaffold_48:2276707...2279071
NR annotation: KAJ7333888.1, hypothetical protein OS493_015981 [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
P0A9G7	Isocitrate lyase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) OX=199310 GN=aceA PE=3 SV=1
P0A9G6	Isocitrate lyase OS=Escherichia coli (strain K12) OX=83333 GN=aceA PE=1 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
IPR006254 all species →	Family	Isocitrate lyase	Interproscan
IPR015813 all species →	Homologous_superfamily	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Interproscan
IPR039556 all species →	Domain	ICL/PEPM domain	Interproscan
IPR018523 all species →	Conserved_site	Isocitrate lyase/phosphorylmutase, conserved site	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:0004451 all species →	Molecular Function	isocitrate lyase activity	Interproscan
GO:0019752 all species →	Biological Process	carboxylic acid metabolic process	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
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_015981-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

6,238.9Max TPM

539.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	30.67	63.20
polyp at pH7 6	18	18	61.66	175.89
coral polyp · control treatment	16	16	269.53	1,157.17
coral polyp · oil and dispersant treatment	16	16	1,155.26	2,737.55
coral polyp · oil treatment	16	16	207.67	473.75
coral polyp · dispersant treatment	16	16	1,943.91	6,238.91
Polyp	10	10	46.08	107.10

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.20
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.51
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.18
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.25
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.69
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.70
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.21
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.83
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.95
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.87
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.67
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.34
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.04
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.82
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.31
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.57
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.57
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.46
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	175.89
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	170.41
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	72.61
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.12
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.55
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.48
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.52
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.53
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.61
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.54
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.17
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.82
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.64
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.98
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.16
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.10
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.11
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.70
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1,157.17
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	512.34
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	451.47
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	436.01
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	353.08
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	259.51
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	211.17
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	197.30
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	136.24
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	134.88
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	131.40
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.70
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.78
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.62
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.35
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.39
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,737.55
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,449.13
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2,063.74
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,799.96
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,756.89
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,310.88
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,150.60
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,012.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,012.59
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	760.87
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	661.43
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	567.39
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	321.82
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	318.67
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	297.10
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	262.63
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	473.75
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	432.72
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	402.13
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	325.51
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	308.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	235.35
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	223.69
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	214.66
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	188.30
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	135.92
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	117.74
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.03
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.57
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.71
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.95
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.16
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6,238.91
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3,929.39
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,998.71
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,335.38
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,069.57
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2,012.60
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,986.00
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,796.27
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,548.69
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,513.18
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,387.45
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,315.99
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	789.97
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	643.23
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	287.03
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	250.25
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	107.10
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	81.98
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	73.97
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	50.82
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	48.93
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	44.47
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	16.11
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.21
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.66
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.55

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.