Gene detail

Detailed information of OS493_002543-T1 in Lophelia pertusa

Genomic Location: scaffold_5:4083799...4118771
NR annotation: KAJ7365822.1, Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase [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
Q5ZM57	Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase OS=Gallus gallus OX=9031 GN=HACD3 PE=2 SV=1
Q7SY06	Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase OS=Danio rerio OX=7955 GN=hacd3 PE=2 SV=2
Q8K2C9	Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 OS=Mus musculus OX=10090 GN=Hacd3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004335 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04387 all species →	PTPLA	Protein tyrosine phosphatase-like protein, PTPLA	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007052 all species →	Domain	CS domain	Interproscan
IPR008978 all species →	Homologous_superfamily	HSP20-like chaperone	Interproscan
IPR007482 all species →	Family	Protein-tyrosine phosphatase-like, PTPLA	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11035 all species →	VERY-LONG-CHAIN (3R)-3-HYDROXYACYL-COA DEHYDRATASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0018812 all species →	Molecular Function	3-hydroxyacyl-CoA dehydratase activity	Interproscan
GO:0030148 all species →	Biological Process	sphingolipid biosynthetic process	Interproscan
GO:0030176 all species →	Cellular Component	obsolete integral component of endoplasmic reticulum membrane	Interproscan
GO:0030497 all species →	Biological Process	fatty acid elongation	Interproscan
GO:0042761 all species →	Biological Process	very long-chain fatty acid biosynthetic 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

No KEGG orthology assignment for OS493_002543-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_002543-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

108TPM > 0

7Conditions

75.7Max TPM

11.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.92	12.36
polyp at pH7 6	18	16	8.13	12.87
coral polyp · control treatment	16	16	12.37	16.90
coral polyp · oil and dispersant treatment	16	16	10.74	17.53
coral polyp · oil treatment	16	16	12.83	18.34
coral polyp · dispersant treatment	16	16	10.99	18.69
Polyp	10	10	18.73	75.72

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.36
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.65
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.47
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.17
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.74
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.69
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.93
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.84
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.68
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.25
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.00
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.88
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.69
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.47
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.04
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.83
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.59
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.18
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.87
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.66
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.58
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.35
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.32
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.06
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.84
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.53
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.30
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.19
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.71
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.71
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.10
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.12
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
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.90
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.99
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.89
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.34
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.23
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.49
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.50
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.20
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.68
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.12
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.71
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.63
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.33
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.29
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.53
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.73
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.10
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.77
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.31
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.51
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.27
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.11
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.80
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.74
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.99
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.63
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.34
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.12
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.06
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.22
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.89
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.32
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.16
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.22
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.83
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.64
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.17
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.13
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.36
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.08
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.69
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.59
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.68
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.27
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.26
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.78
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.19
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.91
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.00
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.65
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.24
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.79
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.22
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.50
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.32
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	75.72
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	50.09
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.37
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.30
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	9.94
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	7.35
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.04
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.51
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.17
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.85

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.