Gene detail

Detailed information of OS493_010298-T1 in Lophelia pertusa

Genomic Location: scaffold_25:817141...818936
NR annotation: KAJ7392647.1, Lysosome-associated membrane glycoprotein 1 [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
P49129	Lysosome-associated membrane glycoprotein 1 OS=Cricetulus griseus OX=10029 GN=LAMP1 PE=2 SV=1
P14562	Lysosome-associated membrane glycoprotein 1 OS=Rattus norvegicus OX=10116 GN=Lamp1 PE=1 SV=1
P11438	Lysosome-associated membrane glycoprotein 1 OS=Mus musculus OX=10090 GN=Lamp1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002080 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21222 all species →	Lamp2_2nd	Lysosome-associated membrane glycoprotein 2, transmembrane segment	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002000 all species →	Family	Lysosome-associated membrane glycoprotein	Interproscan
IPR048524 all species →	Domain	Lysosome-associated membrane glycoprotein 2-like, transmembrane domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11506 all species →	LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005765 all species →	Cellular Component	lysosomal membrane	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0031902 all species →	Cellular Component	late endosome membrane	Interproscan
GO:0072594 all species →	Biological Process	establishment of protein localization to 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_010298-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_010298-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

1,051.0Max TPM

411.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	361.78	528.65
polyp at pH7 6	18	18	414.80	991.45
coral polyp · control treatment	16	16	506.65	728.78
coral polyp · oil and dispersant treatment	16	16	530.29	991.93
coral polyp · oil treatment	16	16	442.66	1,051.03
coral polyp · dispersant treatment	16	16	377.38	666.37
Polyp	10	10	159.78	316.90

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	528.65
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	503.42
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	437.89
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	428.73
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	383.15
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	377.10
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	374.14
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	367.62
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	367.43
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	365.20
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	361.28
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	354.15
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	289.07
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	283.38
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	280.84
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	275.92
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	267.63
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	266.52
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	991.45
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	965.31
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	455.68
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	447.45
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	447.15
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	444.25
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	424.20
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	418.09
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	412.37
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	411.24
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	354.16
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	348.73
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	296.64
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	290.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	246.88
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	233.36
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	146.42
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	132.85
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	728.78
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	728.06
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	727.45
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	706.41
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	620.54
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	602.07
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	542.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	524.48
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	479.95
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	479.12
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	465.79
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	428.31
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	347.71
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	343.73
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	247.64
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	133.44
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	991.93
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	825.30
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	689.83
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	641.89
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	608.35
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	563.38
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	546.18
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	507.71
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	505.61
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	500.57
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	481.19
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	448.99
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	390.44
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	326.37
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	309.67
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	147.25
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1,051.03
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	717.76
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	642.13
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	551.13
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	534.11
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	484.78
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	467.76
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	462.09
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	408.53
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	379.26
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	363.40
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	337.47
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	282.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	209.83
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	155.16
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.04
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	666.37
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	589.90
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	574.49
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	527.62
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	451.36
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	417.76
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	385.17
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	370.58
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	365.26
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	363.67
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	357.25
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	316.11
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	300.56
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	260.25
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	76.01
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.71
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	316.90
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	283.28
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	275.50
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	184.20
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	157.59
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	127.81
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	82.35
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	69.82
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	52.97
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	47.41

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.