Gene detail

Detailed information of OS493_026434-T1 in Lophelia pertusa

Genomic Location: scaffold_136:304378...344617
NR annotation: KAJ7371336.1, sorting nexin 13 [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
Q9Y5W8	Sorting nexin-13 OS=Homo sapiens OX=9606 GN=SNX13 PE=1 SV=4
Q6PHS6	Sorting nexin-13 OS=Mus musculus OX=10090 GN=Snx13 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003876 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02194 all species →	PXA	PXA domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003114 all species →	Domain	Phox-associated domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22775 all species →	SORTING NEXIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005769 all species →	Cellular Component	early endosome	Interproscan
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0043231 all species →	Cellular Component	intracellular membrane-bounded organelle	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_026434-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_026434-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

107TPM > 0

7Conditions

28.4Max TPM

12.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	11.97	27.01
polyp at pH7 6	18	16	11.55	18.91
coral polyp · control treatment	16	16	13.80	22.83
coral polyp · oil and dispersant treatment	16	16	14.25	25.47
coral polyp · oil treatment	16	16	12.70	20.67
coral polyp · dispersant treatment	16	16	16.75	28.41
Polyp	10	9	6.56	14.63

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	-	27.01
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.37
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.07
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.03
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.92
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.92
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.75
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.87
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.76
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.14
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.79
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.78
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.21
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.81
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.78
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.26
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.06
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.91
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.88
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.94
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.83
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.87
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.68
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.91
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.85
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.76
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.05
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.88
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.39
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.46
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.03
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
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.83
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	17.35
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.42
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.98
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.96
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.95
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.90
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.63
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.20
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.11
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.70
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.14
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.84
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.68
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.11
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.47
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.02
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.96
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.17
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.73
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.14
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.55
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.84
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.17
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.90
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.26
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.61
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.95
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.41
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.12
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.68
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.67
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.00
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.80
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.74
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.25
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.96
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.52
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.94
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.66
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.60
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.99
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.90
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.71
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.77
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.91
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.73
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.41
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.72
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.58
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.04
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.70
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.94
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.58
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.46
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.40
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.01
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.76
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.76
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.64
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.35
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.94
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.72
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	14.63
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.14
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	7.08
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.66
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	6.50
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	5.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	4.11
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.16
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.