Gene detail

Detailed information of OS493_011078-T1 in Lophelia pertusa

Genomic Location: scaffold_28:119892...126177
NR annotation: KAJ7373483.1, Sorting nexin-29 [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
Q9D3S3	Sorting nexin-29 OS=Mus musculus OX=10090 GN=Snx29 PE=1 SV=2
Q8TEQ0	Sorting nexin-29 OS=Homo sapiens OX=9606 GN=SNX29 PE=1 SV=3
Q08DX0	Sorting nexin-29 OS=Bos taurus OX=9913 GN=SNX29 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003204 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02759 all species →	RUN	RUN domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004012 all species →	Domain	RUN domain	Interproscan
IPR037213 all species →	Homologous_superfamily	RUN domain superfamily	Interproscan
IPR047329 all species →	Domain	Sorting nexin-29, RUN domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47194 all species →	SORTING NEXIN-29-RELATED	Interproscan

Gene Ontology

No Gene Ontology signature was detected for OS493_011078-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_011078-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_011078-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

88TPM > 0

7Conditions

15.6Max TPM

2.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	9	1.09	3.45
polyp at pH7 6	18	10	1.31	3.88
coral polyp · control treatment	16	16	4.01	8.12
coral polyp · oil and dispersant treatment	16	16	4.35	15.63
coral polyp · oil treatment	16	16	3.48	7.70
coral polyp · dispersant treatment	16	14	3.96	7.75
Polyp	10	7	0.54	1.59

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.45
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.89
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.33
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.10
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.08
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.02
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.67
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.57
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.56
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.88
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.86
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.82
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.27
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.14
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.07
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.05
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.61
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.60
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.36
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.12
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.95
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.93
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.36
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.31
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.01
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.83
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.81
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.56
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.58
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.76
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.59
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.97
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.89
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.36
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.63
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.36
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.23
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.13
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.57
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.26
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.87
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.72
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.45
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.23
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.21
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.93
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.63
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.37
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.09
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.90
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.70
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.65
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.07
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.03
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.00
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.98
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.80
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.72
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.29
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.12
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.05
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.99
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.62
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.59
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.16
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.75
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.50
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.17
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.13
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.90
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.53
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.43
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.10
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.55
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.20
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.18
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.74
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.43
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.59
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.98
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.94
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.62
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.49
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.42
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.40
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
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.