Gene detail

Detailed information of OS493_016170-T1 in Lophelia pertusa

Genomic Location: scaffold_49:1462412...1469319
NR annotation: KAJ7391880.1, intercellular trafficking and secretion [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
Q91YJ2	Sorting nexin-4 OS=Mus musculus OX=10090 GN=Snx4 PE=1 SV=1
Q5R4C2	Sorting nexin-4 OS=Pongo abelii OX=9601 GN=SNX4 PE=2 SV=1
O95219	Sorting nexin-4 OS=Homo sapiens OX=9606 GN=SNX4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006290 (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
IPR027267 all species →	Homologous_superfamily	AH/BAR domain superfamily	Interproscan
IPR036871 all species →	Homologous_superfamily	PX domain superfamily	Interproscan
IPR001683 all species →	Domain	Phox homology	Interproscan
IPR034783 all species →	Family	Sorting nexin-4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46596 all species →	SORTING NEXIN-4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015031 all species →	Biological Process	protein transport	Interproscan
GO:0031201 all species →	Cellular Component	SNARE complex	Interproscan
GO:0031901 all species →	Cellular Component	early endosome membrane	Interproscan
GO:0032266 all species →	Molecular Function	phosphatidylinositol-3-phosphate binding	Interproscan
GO:2000786 all species →	Biological Process	positive regulation of autophagosome assembly	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
K17919	SNX4; sorting nexin-4	-	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_016170-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

38.0Max TPM

19.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	21.20	36.35
polyp at pH7 6	18	18	22.40	28.00
coral polyp · control treatment	16	16	23.12	36.48
coral polyp · oil and dispersant treatment	16	16	17.09	22.33
coral polyp · oil treatment	16	16	20.97	38.00
coral polyp · dispersant treatment	16	16	13.87	23.49
Polyp	10	10	15.94	28.92

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	-	36.35
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.47
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.14
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.41
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.61
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.57
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.12
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.58
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.05
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.71
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.45
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.40
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.11
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.30
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.21
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.71
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.62
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.00
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.95
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.85
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.04
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.02
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.76
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.71
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.62
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.82
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.93
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.56
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.54
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.22
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.14
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.10
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.60
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.28
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.10
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.48
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.49
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.91
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.42
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.51
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.64
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.34
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.49
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.92
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.68
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.16
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.75
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.23
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.01
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.33
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.64
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.59
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.42
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.03
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.59
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.61
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.03
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.81
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.17
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.86
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.66
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.39
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.02
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.36
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.98
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.00
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.01
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.41
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.08
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.52
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.53
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.85
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.84
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.41
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.55
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.49
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.43
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.57
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.72
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.52
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.62
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.49
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.62
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.29
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.55
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.99
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.06
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.56
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.49
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.65
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.36
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.23
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.22
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.96
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.30
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.89
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.20
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	28.92
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	20.03
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	19.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	17.03
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	14.18
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	13.55
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	13.54
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	11.80
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	11.07
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.41

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.