Gene detail

Detailed information of OS493_015332-T1 in Lophelia pertusa

Genomic Location: scaffold_45:1777341...1777919
NR annotation: KAJ7379540.1, hypothetical protein OS493_015332 [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)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009378 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05198 all species →	IF3_N	Translation initiation factor IF-3, N-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036787 all species →	Homologous_superfamily	Translation initiation factor 3 (IF-3), N-terminal domain superfamily	Interproscan
IPR001288 all species →	Family	Translation initiation factor 3	Interproscan
IPR036788 all species →	Homologous_superfamily	Translation initiation factor 3 (IF-3), C-terminal domain superfamily	Interproscan
IPR019814 all species →	Domain	Translation initiation factor 3, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10938 all species →	TRANSLATION INITIATION FACTOR IF-3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003743 all species →	Molecular Function	translation initiation factor activity	Interproscan
GO:0006413 all species →	Biological Process	translational initiation	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0032790 all species →	Biological Process	ribosome disassembly	Interproscan
GO:0043022 all species →	Molecular Function	ribosome binding	Interproscan
GO:0070124 all species →	Biological Process	mitochondrial translational initiation	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_015332-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_015332-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

35.2Max TPM

10.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.09	14.47
polyp at pH7 6	18	18	11.96	21.33
coral polyp · control treatment	16	16	14.44	35.24
coral polyp · oil and dispersant treatment	16	16	11.01	20.93
coral polyp · oil treatment	16	16	11.85	20.53
coral polyp · dispersant treatment	16	16	5.13	11.54
Polyp	10	10	12.11	23.23

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.47
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.23
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.95
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.59
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.91
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.73
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.30
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.96
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.86
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.81
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.44
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.42
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.38
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.00
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.96
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.71
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.57
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.25
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.33
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.70
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.03
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.46
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.74
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.08
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.40
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.30
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.42
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.36
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.64
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.04
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.03
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.99
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.75
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.28
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.86
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.24
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.21
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.56
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.51
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.67
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.87
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.79
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.76
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.78
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.97
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.14
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.06
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.70
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.68
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.67
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.43
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.93
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.66
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.08
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.97
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.49
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.28
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.96
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.13
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.38
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.78
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.65
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.07
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.62
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.87
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.92
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.37
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.53
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.09
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.08
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.45
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.64
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.21
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.73
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.67
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.51
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.16
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.04
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.56
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.38
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.03
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.33
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.27
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.54
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.42
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.11
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.60
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.50
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.06
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.75
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.72
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.20
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.86
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.80
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.11
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.10
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.76
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.51
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.99
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	23.23
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	14.92
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	14.44
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	13.24
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.70
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	11.11
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	9.53
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	8.30
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	7.49
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.12

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.