Gene detail

Detailed information of OS493_006050-T1 in Lophelia pertusa

Genomic Location: scaffold_12:4069508...4081261
NR annotation: KAJ7339643.1, Protein smg5 [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
F1R7R1	Nonsense-mediated mRNA decay factor SMG5 OS=Danio rerio OX=7955 GN=smg5 PE=2 SV=1
Q9UPR3	Nonsense-mediated mRNA decay factor SMG5 OS=Homo sapiens OX=9606 GN=SMG5 PE=1 SV=3
Q6ZPY2	Nonsense-mediated mRNA decay factor SMG5 OS=Mus musculus OX=10090 GN=Smg5 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006483 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10373 all species →	EST1_DNA_bind	Est1 DNA/RNA binding domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045153 all species →	Family	Est1/Ebs1-like	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR018834 all species →	Domain	DNA/RNA-binding domain, Est1-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15696 all species →	SMG-7 SUPPRESSOR WITH MORPHOLOGICAL EFFECT ON GENITALIA PROTEIN 7	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0005697 all species →	Cellular Component	telomerase holoenzyme complex	Interproscan
GO:0042162 all species →	Molecular Function	telomeric DNA binding	Interproscan
GO:0070034 all species →	Molecular Function	telomerase RNA binding	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_006050-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_006050-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

41.9Max TPM

19.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	17.92	30.98
polyp at pH7 6	18	18	16.19	25.65
coral polyp · control treatment	16	16	28.63	41.86
coral polyp · oil and dispersant treatment	16	16	26.58	37.66
coral polyp · oil treatment	16	16	22.58	31.63
coral polyp · dispersant treatment	16	16	14.14	20.60
Polyp	10	10	8.61	14.10

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.98
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.04
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.79
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.84
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.51
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.08
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.32
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.28
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.77
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.49
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.00
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.70
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.84
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.57
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.62
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.09
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.60
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.65
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.19
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.29
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.13
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.02
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.94
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.48
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.53
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.42
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.06
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.26
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.19
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.65
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.20
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.72
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.32
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.63
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.86
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.37
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.88
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.94
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.07
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.34
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.77
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.38
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.30
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.03
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.07
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.37
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.91
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.85
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.35
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.55
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.66
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.68
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.29
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.74
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.22
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.88
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.16
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.80
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.86
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.35
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.31
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.18
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.85
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.31
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.01
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.63
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.11
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.80
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.17
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.31
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.87
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.72
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.95
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.70
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.07
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.32
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.70
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.03
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.86
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.21
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.60
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.71
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.28
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.76
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.65
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.39
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.38
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.25
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.84
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.64
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.94
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.26
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.97
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.83
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.88
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.84
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.10
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	12.97
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.94
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.74
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	9.58
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	6.92
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.22
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.39
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	4.67
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.57

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.