Gene detail

Detailed information of OS493_002478-T1 in Lophelia pertusa

Genomic Location: scaffold_5:2800821...2822845
NR annotation: KAJ7365761.1, Thioredoxin-like protein 1 [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
Q7KQL8	Thioredoxin 1 OS=Plasmodium falciparum (isolate 3D7) OX=36329 GN=TRX1 PE=1 SV=1
Q9UW02	Thioredoxin OS=Coprinus comatus OX=56187 PE=1 SV=1
P22217	Thioredoxin-1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TRX1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006386 (this species only)
Ubiquitin family	ULD\|UFD\|UBX · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00085 all species →	Thioredoxin	Thioredoxin	Domain	Interproscan
PF00789 all species →	UBX	UBX domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013766 all species →	Domain	Thioredoxin domain	Interproscan
IPR001012 all species →	Domain	UBX domain	Interproscan
IPR009060 all species →	Homologous_superfamily	UBA-like superfamily	Interproscan
IPR036249 all species →	Homologous_superfamily	Thioredoxin-like superfamily	Interproscan
IPR050620 all species →	Family	Thioredoxin-like	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10438 all species →	THIOREDOXIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	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_002478-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_002478-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

109TPM > 0

7Conditions

49.2Max TPM

18.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	17.56	23.87
polyp at pH7 6	18	18	16.68	21.12
coral polyp · control treatment	16	16	25.56	42.18
coral polyp · oil and dispersant treatment	16	16	20.46	49.19
coral polyp · oil treatment	16	16	21.29	31.80
coral polyp · dispersant treatment	16	16	17.16	26.87
Polyp	10	9	8.90	18.29

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	-	23.87
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.23
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.19
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.96
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.43
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.11
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.25
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.45
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.41
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.33
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.12
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.65
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.97
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.71
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.12
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.67
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.84
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.82
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.12
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.01
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.30
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.56
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.38
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.94
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.85
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.82
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.48
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.40
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.07
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.89
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.04
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.88
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.23
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.18
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.41
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.75
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.07
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.38
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.78
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.68
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.33
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.75
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.60
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.69
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.51
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.59
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.39
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.52
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.26
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.19
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.41
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.33
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.27
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.10
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.09
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.63
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.64
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.03
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.40
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.72
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.64
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.77
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.79
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.12
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.15
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.80
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.36
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.96
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.01
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.58
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.65
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.54
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.25
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.69
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.85
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.67
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.84
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.67
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.19
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.96
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.64
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.87
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.46
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.90
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.26
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.39
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.82
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.73
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.46
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.20
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.52
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.27
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.54
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.84
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.20
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.79
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.37
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	18.29
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	17.01
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	11.71
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.62
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.24
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.59
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.77
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.48
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.28
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.