Gene detail

Detailed information of OS493_002948-T1 in Lophelia pertusa

Genomic Location: scaffold_6:2558288...2565396
NR annotation: KAJ7340216.1, THO complex subunit 6 [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
Q5U4D9	THO complex subunit 6 homolog OS=Mus musculus OX=10090 GN=Thoc6 PE=1 SV=1
Q6AY87	THO complex subunit 6 homolog OS=Rattus norvegicus OX=10116 GN=Thoc6 PE=2 SV=1
Q5XJS5	THO complex subunit 6 homolog OS=Danio rerio OX=7955 GN=thoc6 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005827 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR042626 all species →	Family	THO complex subunit 6	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR44411 all species →	THO COMPLEX SUBUNIT 6 HOMOLOG	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000346 all species →	Cellular Component	transcription export complex	Interproscan
GO:0000347 all species →	Cellular Component	THO complex	Interproscan
GO:0006406 all species →	Biological Process	mRNA export from nucleus	Interproscan
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_002948-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_002948-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

39.0Max TPM

11.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.88	24.46
polyp at pH7 6	18	18	12.79	23.38
coral polyp · control treatment	16	16	9.75	22.59
coral polyp · oil and dispersant treatment	16	16	10.77	39.01
coral polyp · oil treatment	16	16	9.33	15.62
coral polyp · dispersant treatment	16	16	9.60	33.83
Polyp	10	10	15.82	28.07

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	-	24.46
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.61
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.59
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.80
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.64
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.51
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.04
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.91
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.84
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.60
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.12
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.82
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.79
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.45
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.41
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.34
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.06
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.80
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.38
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.13
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.69
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.12
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.40
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.35
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.34
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.99
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.41
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.27
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.85
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.28
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.44
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.20
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.23
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.40
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.14
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.63
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.59
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.89
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.24
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.43
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.64
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.51
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.02
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.11
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.74
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.20
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.96
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.94
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.90
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.58
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.10
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.14
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.01
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.16
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.56
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.48
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.34
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.06
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.02
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.53
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.20
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.50
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.06
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.16
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.09
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.29
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.62
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.84
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.55
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.54
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.50
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.76
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.41
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.19
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.15
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.67
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.23
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.16
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.93
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.20
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.84
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.71
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.83
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.66
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.20
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.85
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.13
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.11
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.38
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.54
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.60
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.96
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.46
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.16
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.02
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.66
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.08
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.02
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	28.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	26.03
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	19.70
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.74
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.84
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	14.52
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.74
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	10.94
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.61
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.02

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.