Gene detail

Detailed information of OS493_007450-T1 in Lophelia pertusa

Genomic Location: scaffold_16:2560375...2573164
NR annotation: KAJ7374361.1, Sorting nexin-5 [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
Q9UNH7	Sorting nexin-6 OS=Homo sapiens OX=9606 GN=SNX6 PE=1 SV=1
Q6P8X1	Sorting nexin-6 OS=Mus musculus OX=10090 GN=Snx6 PE=1 SV=2
Q5R613	Sorting nexin-6 OS=Pongo abelii OX=9601 GN=SNX6 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006166 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00787 all species →	PX	PX domain	Domain	Interproscan
PF09325 all species →	Vps5	Vps5 C terminal like	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001683 all species →	Domain	Phox homology	Interproscan
IPR036871 all species →	Homologous_superfamily	PX domain superfamily	Interproscan
IPR015404 all species →	Domain	Sorting nexin/Vps5-like, C-terminal	Interproscan
IPR014637 all species →	Family	Sorting nexin-5/6/32	Interproscan
IPR027267 all species →	Homologous_superfamily	AH/BAR domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45850 all species →	SORTING NEXIN FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K17920	SNX5_6_32; sorting nexin-5/6/32	-	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_007450-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

120.5Max TPM

64.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	57.52	73.35
polyp at pH7 6	18	18	59.69	75.09
coral polyp · control treatment	16	16	81.59	120.55
coral polyp · oil and dispersant treatment	16	16	70.74	103.31
coral polyp · oil treatment	16	16	71.11	118.07
coral polyp · dispersant treatment	16	16	56.15	82.33
Polyp	10	10	54.69	80.69

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	-	73.35
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.75
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.60
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.54
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.81
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	65.16
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.35
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.89
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.88
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.82
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.56
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.55
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.40
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.78
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.89
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.38
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.82
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.90
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.09
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	71.59
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.26
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.18
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.83
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	66.49
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.86
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.61
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.88
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.94
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.73
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.74
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.63
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.48
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.30
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.48
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	120.55
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	107.38
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.88
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	98.35
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.84
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.73
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.89
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.57
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.04
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.94
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.95
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.87
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.62
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.74
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.03
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.12
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	103.31
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	95.21
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	94.21
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	82.32
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.29
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.82
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.24
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	73.85
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.83
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	69.01
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.51
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	65.73
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.99
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.68
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.70
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.14
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	118.07
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	97.76
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	88.47
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	84.33
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	83.61
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	82.66
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	81.72
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	79.03
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.08
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.50
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.66
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.59
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.11
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.12
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.08
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.95
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.33
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	80.75
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.98
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.90
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.88
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.04
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.93
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.33
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.20
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.07
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.05
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.39
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.57
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.15
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.70
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	80.69
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	66.89
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	63.21
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	61.85
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	60.68
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	54.89
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	52.35
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	40.20
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	39.28
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	26.85

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.