Gene detail

Detailed information of OS493_007972-T1 in Lophelia pertusa

Genomic Location: scaffold_18:2334039...2373449
NR annotation: KAJ7337815.1, Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial [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
Q5XIT9	Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial OS=Rattus norvegicus OX=10116 GN=Mccc2 PE=2 SV=1
Q3ULD5	Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial OS=Mus musculus OX=10090 GN=Mccc2 PE=1 SV=1
Q9HCC0	Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial OS=Homo sapiens OX=9606 GN=MCCC2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001327 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01039 all species →	Carboxyl_trans	Carboxyl transferase domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045190 all species →	Family	Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like	Interproscan
IPR011763 all species →	Domain	Acetyl-coenzyme A carboxyltransferase, C-terminal	Interproscan
IPR034733 all species →	Domain	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Interproscan
IPR029045 all species →	Homologous_superfamily	ClpP/crotonase-like domain superfamily	Interproscan
IPR011762 all species →	Domain	Acetyl-coenzyme A carboxyltransferase, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22855 all species →	ACETYL, PROPIONYL, PYRUVATE, AND GLUTACONYL CARBOXYLASE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004485 all species →	Molecular Function	methylcrotonoyl-CoA carboxylase activity	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006552 all species →	Biological Process	L-leucine catabolic process	Interproscan
GO:1905202 all species →	Cellular Component	methylcrotonoyl-CoA carboxylase complex	Interproscan
GO:0016874 all species →	Molecular Function	ligase 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
K01969	MCCC2, accD1; 3-methylcrotonyl-CoA carboxylase beta subunit	EC:6.4.1.4	Valine, leucine and isoleucine degradation	ko00280	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_007972-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

39.5Max TPM

18.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	19.80	23.75
polyp at pH7 6	18	18	21.31	27.50
coral polyp · control treatment	16	16	20.61	38.52
coral polyp · oil and dispersant treatment	16	16	15.33	26.68
coral polyp · oil treatment	16	16	21.17	39.47
coral polyp · dispersant treatment	16	16	15.45	30.08
Polyp	10	10	15.95	24.14

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.75
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.15
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.73
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.01
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.61
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.50
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.60
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.67
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.66
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.54
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.49
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.08
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.99
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.76
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.12
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.08
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.69
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.50
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.73
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.42
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.20
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.67
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.13
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.24
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.07
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.84
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.36
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.16
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.86
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.18
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.90
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.17
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.52
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.98
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.84
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.75
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.96
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.58
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.19
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.79
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.76
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.36
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.32
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.69
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.95
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.41
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.98
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.68
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.03
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.27
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.25
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.30
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.73
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.50
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.69
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.69
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.65
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.59
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.57
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.47
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.57
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.22
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.92
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.70
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.55
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.33
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.43
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.58
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.78
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.23
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.82
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.68
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.47
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.88
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.08
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.08
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.29
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.85
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.56
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.20
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.26
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.37
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.63
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.19
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.97
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.69
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.70
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.91
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.73
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.91
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.82
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	24.14
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	21.13
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	20.76
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	20.35
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	19.57
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	14.42
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.96
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.47
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	9.44
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.22

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.