Gene detail

Detailed information of OS493_009223-T1 in Lophelia pertusa

Genomic Location: scaffold_22:1020895...1022187
NR annotation: KAJ7373899.1, hypothetical protein OS493_009223 [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
Q40082	Xylose isomerase OS=Hordeum vulgare OX=4513 GN=XYLA PE=1 SV=1
Q9FKK7	Xylose isomerase OS=Arabidopsis thaliana OX=3702 GN=XYLA PE=2 SV=2
Q7UVG2	Xylose isomerase OS=Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1) OX=243090 GN=xylA PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0010532 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_009223-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR001998 all species →	Family	Xylose isomerase	Interproscan
IPR036237 all species →	Homologous_superfamily	Xylose isomerase-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR48320 all species →	-	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005975 all species →	Biological Process	carbohydrate metabolic process	Interproscan
GO:0009045 all species →	Molecular Function	xylose isomerase 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

No KEGG orthology assignment for OS493_009223-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_009223-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

103TPM > 0

7Conditions

18.7Max TPM

7.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	15	7.33	15.32
polyp at pH7 6	18	16	10.22	18.67
coral polyp · control treatment	16	16	8.39	16.26
coral polyp · oil and dispersant treatment	16	16	6.17	13.78
coral polyp · oil treatment	16	16	6.69	9.46
coral polyp · dispersant treatment	16	16	6.88	11.90
Polyp	10	8	5.40	15.96

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	-	15.32
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.75
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.38
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.29
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.50
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.40
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.35
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.18
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.55
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.04
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.35
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.38
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.83
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.91
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.67
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.41
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.02
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.68
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.13
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.27
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.42
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.39
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.14
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.14
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.54
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.95
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.86
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.59
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.88
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
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.26
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.11
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.65
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.53
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.34
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.52
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.50
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.15
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.40
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.98
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.83
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.82
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.62
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.20
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.62
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.75
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.78
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.36
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.95
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.78
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.81
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.66
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.82
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.80
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.54
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.37
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.13
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.40
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.45
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.39
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.17
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.46
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.12
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.93
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.89
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.33
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.90
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.66
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.59
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.45
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.19
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.65
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.01
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.70
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.41
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.74
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.06
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.90
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.60
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.21
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.50
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.39
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.22
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.40
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.37
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.21
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.63
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.31
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.98
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.55
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.73
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.63
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	15.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	10.44
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	7.54
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	5.52
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.40
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.66
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.90
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.57
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.