Gene detail

Detailed information of OS493_004428-T1 in Lophelia pertusa

Genomic Location: scaffold_8:6424092...6426657
NR annotation: KAJ7387431.1, hypothetical protein OS493_004428 [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
Q8RQN6	Isocitrate lyase OS=Corynebacterium efficiens (strain DSM 44549 / YS-314 / AJ 12310 / JCM 11189 / NBRC 100395) OX=196164 GN=aceA PE=3 SV=4

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
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
IPR015813 all species →	Homologous_superfamily	Pyruvate/Phosphoenolpyruvate 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_004428-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

1,814.7Max TPM

192.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	1.63	3.18
polyp at pH7 6	18	18	7.42	29.33
coral polyp · control treatment	16	16	89.71	670.84
coral polyp · oil and dispersant treatment	16	16	495.15	1,677.28
coral polyp · oil treatment	16	16	78.79	293.05
coral polyp · dispersant treatment	16	16	639.41	1,814.73
Polyp	10	10	11.32	80.10

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.18
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.77
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.77
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.46
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.41
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.38
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.33
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.29
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.18
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.04
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.30
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.98
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.51
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.43
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.40
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.34
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.18
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.97
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.26
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.87
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.61
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.60
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.07
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.67
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.99
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.76
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.75
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.64
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.61
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.28
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.76
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.52
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.40
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	670.84
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	212.71
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	180.51
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	110.90
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	110.35
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.95
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.10
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.50
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.34
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.91
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.09
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.04
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.86
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.83
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.79
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.62
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,677.28
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,271.80
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1,181.05
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	741.64
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	594.04
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	418.01
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	398.50
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	365.01
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	273.62
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	268.77
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	216.05
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	215.31
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	143.69
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	80.04
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.63
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	293.05
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	151.82
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	115.89
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.26
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	107.63
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	102.33
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	86.50
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.59
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.99
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.90
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.47
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.11
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.13
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.86
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.18
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.96
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,814.73
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,098.60
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1,060.14
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	988.47
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	903.48
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	747.01
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	518.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	517.46
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	493.25
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	481.87
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	451.35
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	380.92
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	305.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	270.95
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	170.61
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.35
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	80.10
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	15.31
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.25
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.06
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.62
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.44
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.32
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.61
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.52

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.