Gene detail

Detailed information of OS493_018719-T1 in Lophelia pertusa

Genomic Location: scaffold_62:1602262...1613572
NR annotation: KAJ7385026.1, hypothetical protein OS493_018719 [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
Q8K0C9	GDP-mannose 4,6 dehydratase OS=Mus musculus OX=10090 GN=Gmds PE=1 SV=1
Q8K3X3	GDP-mannose 4,6 dehydratase OS=Cricetulus griseus OX=10029 GN=GMDS PE=2 SV=1
O60547	GDP-mannose 4,6 dehydratase OS=Homo sapiens OX=9606 GN=GMDS PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003533 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16363 all species →	GDP_Man_Dehyd	GDP-mannose 4,6 dehydratase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016040 all species →	Domain	NAD(P)-binding domain	Interproscan
IPR006368 all species →	Family	GDP-mannose 4,6-dehydratase	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43715 all species →	GDP-MANNOSE 4,6-DEHYDRATASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008446 all species →	Molecular Function	GDP-mannose 4,6-dehydratase activity	Interproscan
GO:0019673 all species →	Biological Process	GDP-mannose metabolic process	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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
K01711	gmd, GMDS; GDPmannose 4,6-dehydratase	EC:4.2.1.47	O-Antigen nucleotide sugar biosynthesis	ko00541	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_018719-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

53.2Max TPM

28.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	30.29	48.56
polyp at pH7 6	18	18	30.32	53.23
coral polyp · control treatment	16	16	28.58	42.95
coral polyp · oil and dispersant treatment	16	16	27.26	47.36
coral polyp · oil treatment	16	16	31.02	52.20
coral polyp · dispersant treatment	16	16	26.34	49.12
Polyp	10	10	19.61	32.42

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	-	48.56
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.97
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.83
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.18
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.40
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.01
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.40
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.76
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.92
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.86
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.64
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.38
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.80
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.14
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.55
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.40
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.23
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.30
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.30
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.36
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.55
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.02
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.54
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.49
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.20
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.66
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.43
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.39
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.47
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.45
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.13
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.81
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.01
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.48
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.95
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.54
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.57
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.10
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.34
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.31
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.96
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.87
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.94
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.00
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.44
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.29
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.77
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.45
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.74
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.96
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.36
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.45
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.68
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.07
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.74
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.39
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.87
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.90
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.85
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.68
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.35
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.44
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.55
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.53
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.74
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.61
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.51
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.86
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.92
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.94
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.23
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.17
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.36
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.73
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.66
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.68
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.42
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.09
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.72
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.53
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.33
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.12
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.93
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.54
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.97
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.64
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.06
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.78
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.19
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.21
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.36
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.46
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.23
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.48
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.37
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.01
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.19
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	32.42
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	30.45
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	28.18
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	25.10
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	21.59
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.05
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	14.81
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.43
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	9.01
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.03

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.