Gene detail

Detailed information of OS493_009618-T1 in Lophelia pertusa

Genomic Location: scaffold_23:797373...800758
NR annotation: KAJ7363463.1, Sorting nexin-12 [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
Q9UMY4	Sorting nexin-12 OS=Homo sapiens OX=9606 GN=SNX12 PE=1 SV=4
Q1RMH8	Sorting nexin-3 OS=Bos taurus OX=9913 GN=SNX3 PE=2 SV=3
O60493	Sorting nexin-3 OS=Homo sapiens OX=9606 GN=SNX3 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001015 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00787 all species →	PX	PX domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001683 all species →	Domain	Phox homology	Interproscan
IPR036871 all species →	Homologous_superfamily	PX domain superfamily	Interproscan
IPR051074 all species →	Family	Sorting Nexin	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45963 all species →	RE52028P	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0030904 all species →	Cellular Component	retromer complex	Interproscan
GO:0031901 all species →	Cellular Component	early endosome membrane	Interproscan
GO:0032266 all species →	Molecular Function	phosphatidylinositol-3-phosphate binding	Interproscan
GO:0032456 all species →	Biological Process	endocytic recycling	Interproscan
GO:0034499 all species →	Biological Process	late endosome to Golgi transport	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K17918	SNX3_12; sorting nexin-3/12	-	Domain-containing proteins not elsewhere classified	ko04990	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_009618-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

109TPM > 0

7Conditions

106.3Max TPM

41.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	35.26	51.08
polyp at pH7 6	18	18	42.21	66.44
coral polyp · control treatment	16	16	53.61	79.56
coral polyp · oil and dispersant treatment	16	16	45.95	106.33
coral polyp · oil treatment	16	16	45.26	81.35
coral polyp · dispersant treatment	16	16	39.80	71.65
Polyp	10	9	21.44	47.96

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.08
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.19
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.09
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	43.72
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.73
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.54
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.49
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.31
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.31
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.26
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.03
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.74
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.60
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.98
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.47
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.11
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.17
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.92
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.44
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.33
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.74
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.09
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.07
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.55
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.08
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.85
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.08
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.18
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.13
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.34
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.22
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.48
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.76
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.68
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.38
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.31
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.56
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.91
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.70
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	74.57
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.62
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.89
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.77
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.56
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.18
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.31
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.29
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.41
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	42.19
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.49
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.68
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.68
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.33
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.44
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.95
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.18
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.45
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.73
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.78
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.75
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.77
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.15
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.78
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.80
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.24
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.02
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.83
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.98
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	81.35
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.33
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.75
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.40
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.07
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.06
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.11
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.67
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.92
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.26
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.88
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.80
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.78
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.65
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.96
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.69
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.58
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.14
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.04
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.97
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.64
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.43
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.40
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.56
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.75
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.79
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.00
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.61
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	47.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	37.14
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	31.22
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	20.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	19.02
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	18.92
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	17.85
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.55
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	9.30
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.