Gene detail

Detailed information of OS493_006049-T1 in Lophelia pertusa

Genomic Location: scaffold_12:4062141...4069481
NR annotation: KAJ7339642.1, 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
Q6ZPY2	Nonsense-mediated mRNA decay factor SMG5 OS=Mus musculus OX=10090 GN=Smg5 PE=1 SV=2
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

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
PF13638 all species →	PIN_4	PIN domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018834 all species →	Domain	DNA/RNA-binding domain, Est1-type	Interproscan
IPR045153 all species →	Family	Est1/Ebs1-like	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR002716 all species →	Domain	PIN domain	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_006049-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_006049-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

59.9Max TPM

31.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	31.95	49.02
polyp at pH7 6	18	18	29.16	39.88
coral polyp · control treatment	16	16	42.56	59.93
coral polyp · oil and dispersant treatment	16	16	41.44	56.86
coral polyp · oil treatment	16	16	36.69	44.12
coral polyp · dispersant treatment	16	16	19.31	28.66
Polyp	10	10	16.51	24.14

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.02
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.90
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.36
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.24
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.50
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.86
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.74
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.89
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.25
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.55
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.86
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.19
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.09
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.52
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.58
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.07
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.89
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.88
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.96
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.92
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.63
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.30
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.72
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.78
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.08
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.11
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.25
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.28
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.54
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.12
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.04
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.85
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.07
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.93
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.47
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.58
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.31
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.57
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.34
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.40
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.20
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.78
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.85
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.51
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.74
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.22
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.56
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.63
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.86
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.86
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.48
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.83
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.95
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.58
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.01
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.38
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.99
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.43
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.61
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.61
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.60
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.98
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.80
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.39
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.58
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.12
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.51
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.40
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.27
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.81
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.34
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.33
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.18
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.88
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.41
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.88
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.10
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.92
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.49
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.39
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.02
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.66
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.22
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.96
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.39
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.34
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.27
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.95
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.90
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.70
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.67
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.59
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.07
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.81
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.14
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	24.14
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	23.98
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	22.15
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	22.07
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	20.69
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.45
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	14.42
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	9.08
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	7.22
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.84

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.