Gene detail

Detailed information of OS493_029900-T1 in Lophelia pertusa

Genomic Location: scaffold_186:428645...444798
NR annotation: KAJ7325352.1, hypothetical protein OS493_029900 [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
Q08D83	Reticulon-3 OS=Bos taurus OX=9913 GN=RTN3 PE=2 SV=1
Q5RBL9	Reticulon-3 OS=Pongo abelii OX=9601 GN=RTN3 PE=2 SV=1
Q6RJR6	Reticulon-3 OS=Rattus norvegicus OX=10116 GN=Rtn3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002033 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02453 all species →	Reticulon	Reticulon	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003388 all species →	Domain	Reticulon	Interproscan
IPR046964 all species →	Family	Reticulon 1-4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45799 all species →	RETICULON-LIKE PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005789 all species →	Cellular Component	endoplasmic reticulum membrane	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_029900-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_029900-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

108TPM > 0

7Conditions

78.5Max TPM

22.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	26.39	37.98
polyp at pH7 6	18	17	25.42	50.01
coral polyp · control treatment	16	16	20.49	33.49
coral polyp · oil and dispersant treatment	16	16	18.89	36.92
coral polyp · oil treatment	16	16	22.19	35.74
coral polyp · dispersant treatment	16	16	18.44	34.73
Polyp	10	9	29.73	78.49

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.98
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.80
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.26
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.79
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.66
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.26
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.23
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.92
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.72
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.86
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.93
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.35
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.44
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.45
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.28
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.18
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.96
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.01
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.13
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.50
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.65
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.49
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.14
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.64
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.13
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.40
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.80
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.21
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.25
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.08
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.42
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.53
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.49
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.95
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.72
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.93
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.60
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.90
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.45
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.04
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.60
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.47
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.81
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.41
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.99
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.79
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.70
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.92
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.55
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.51
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.23
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.25
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.67
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.07
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.89
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.13
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.96
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.30
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.73
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.69
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.49
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.22
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.63
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.74
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.62
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.88
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.26
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.81
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.68
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.06
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.18
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.59
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.53
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.50
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.56
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.54
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.58
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.46
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.98
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.73
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.31
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.79
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.69
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.33
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.19
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.93
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.85
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.98
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.48
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.69
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.30
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.15
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.95
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.35
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	78.49
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	51.76
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	45.53
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	39.27
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	39.16
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	24.70
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.76
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.50
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.11
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.