Gene detail

Detailed information of OS493_034578-T1 in Lophelia pertusa

Genomic Location: scaffold_295:15506...17249
NR annotation: KAJ7388946.1, sorting nexin-2 [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
Q2TBW7	Sorting nexin-2 OS=Bos taurus OX=9913 GN=SNX2 PE=2 SV=1
O60749	Sorting nexin-2 OS=Homo sapiens OX=9606 GN=SNX2 PE=1 SV=2
Q9CWK8	Sorting nexin-2 OS=Mus musculus OX=10090 GN=Snx2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006131 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09325 all species →	Vps5	Vps5 C terminal like	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027267 all species →	Homologous_superfamily	AH/BAR domain superfamily	Interproscan
IPR015404 all species →	Domain	Sorting nexin/Vps5-like, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10555 all species →	SORTING NEXIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005768 all species →	Cellular Component	endosome	Interproscan
GO:0010008 all species →	Cellular Component	endosome membrane	Interproscan
GO:0034498 all species →	Biological Process	early endosome to Golgi transport	Interproscan
GO:0035091 all species →	Molecular Function	phosphatidylinositol 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_034578-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_034578-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

240.2Max TPM

101.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	97.42	130.23
polyp at pH7 6	18	18	112.29	210.51
coral polyp · control treatment	16	16	101.62	139.15
coral polyp · oil and dispersant treatment	16	16	105.80	135.04
coral polyp · oil treatment	16	16	103.48	141.65
coral polyp · dispersant treatment	16	16	68.64	103.99
Polyp	10	10	128.28	240.19

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	130.23
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	129.24
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	127.10
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	125.22
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	120.36
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	120.32
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	116.50
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	110.05
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	108.92
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	107.34
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	87.32
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	82.92
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	78.79
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	71.89
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.30
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.49
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.72
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.86
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	210.51
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	210.19
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	136.38
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	135.23
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	128.69
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	124.85
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	119.19
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	115.02
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	110.50
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	101.10
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	93.66
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	90.45
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	89.31
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.39
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.54
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.17
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.42
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	139.15
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	133.87
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.99
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	126.54
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	110.86
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	106.20
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	104.96
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.69
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.68
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	92.04
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	91.15
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	88.28
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.03
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.30
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	72.56
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.65
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	135.04
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	134.07
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	131.36
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	130.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	113.55
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.77
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	112.31
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	102.33
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.48
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.15
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.69
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	91.07
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	90.35
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.64
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.74
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.03
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	141.65
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	131.18
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	126.78
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	120.73
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	120.56
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	114.54
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	111.34
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	99.54
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.83
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.68
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.68
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.15
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	87.29
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.37
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	70.13
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.21
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	103.99
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	99.30
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	83.11
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.70
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.22
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.49
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.71
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.67
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	65.61
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.83
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.21
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.67
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.27
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.78
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.68
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	240.19
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	176.76
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	146.36
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	134.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	126.11
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	114.58
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	112.43
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	109.62
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	68.42
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	54.03

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.