Gene detail

Detailed information of OS493_008727-T1 in Lophelia pertusa

Genomic Location: scaffold_20:3525972...3527419
NR annotation: KAJ7386580.1, Exosome RNA helicase MTR4 [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
P42285	Exosome RNA helicase MTR4 OS=Homo sapiens OX=9606 GN=MTREX PE=1 SV=3
Q9CZU3	Exosome RNA helicase MTR4 OS=Mus musculus OX=10090 GN=Mtrex PE=1 SV=1
P47047	ATP-dependent RNA helicase DOB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=MTR4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001225 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13234 all species →	MTR4_beta-barrel	Mtr4-like, beta-barrel domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR025696 all species →	Domain	Exosome RNA helicase MTR4-like, beta-barrel domain	Interproscan

PANTHER

No PANTHER signature was detected for OS493_008727-T1. This gene does have a gene model — the search simply returned no hit.

Gene Ontology

No Gene Ontology signature was detected for OS493_008727-T1. This gene does have a gene model — the search simply returned no hit.

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_008727-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_008727-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

91.2Max TPM

17.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.54	30.31
polyp at pH7 6	18	18	15.36	26.13
coral polyp · control treatment	16	16	23.62	42.13
coral polyp · oil and dispersant treatment	16	16	23.80	91.19
coral polyp · oil treatment	16	16	16.92	27.18
coral polyp · dispersant treatment	16	16	15.71	39.20
Polyp	10	9	7.29	14.36

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.31
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.39
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.11
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.54
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.90
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.61
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.72
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.83
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.40
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.31
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.53
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.06
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.27
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.97
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.79
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.81
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.95
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.27
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.13
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.31
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.53
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.26
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.35
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.27
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.23
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.20
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.98
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.89
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.30
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.18
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.84
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.65
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.51
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.10
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.91
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.13
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.08
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.72
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.17
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.05
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.94
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.32
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.60
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.39
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.22
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.22
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.80
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.54
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.26
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.26
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.24
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.19
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.72
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.41
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.43
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.83
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.81
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.48
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.34
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.60
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.52
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.64
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.01
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.63
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.99
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.18
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.93
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.86
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.21
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.67
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.41
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.50
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.16
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.59
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.95
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.30
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.01
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.00
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.34
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.08
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.20
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.48
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.49
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.77
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.97
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.30
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.96
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.92
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.02
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.62
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.18
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.79
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.40
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.39
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	14.36
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	9.12
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	8.78
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.23
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.99
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.97
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.89
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	5.78
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.77
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.