Gene detail

Detailed information of OS493_016447-T1 in Lophelia pertusa

Genomic Location: scaffold_50:1566641...1578231
NR annotation: KAJ7385367.1, Secretory carrier-associated membrane protein 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
O77735	Secretory carrier-associated membrane protein 1 OS=Sus scrofa OX=9823 GN=SCAMP1 PE=2 SV=1
P56603	Secretory carrier-associated membrane protein 1 OS=Rattus norvegicus OX=10116 GN=Scamp1 PE=1 SV=1
O15126	Secretory carrier-associated membrane protein 1 OS=Homo sapiens OX=9606 GN=SCAMP1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002763 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04144 all species →	SCAMP	SCAMP family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007273 all species →	Family	SCAMP	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10687 all species →	SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN SCAMP	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015031 all species →	Biological Process	protein transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0032588 all species →	Cellular Component	trans-Golgi network membrane	Interproscan
GO:0055038 all species →	Cellular Component	recycling endosome membrane	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
K19995	SCAMP; secretory carrier-associated membrane protein	-	Membrane trafficking	ko04131	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_016447-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

412.9Max TPM

79.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	38.36	69.13
polyp at pH7 6	18	18	38.61	65.97
coral polyp · control treatment	16	16	84.55	138.58
coral polyp · oil and dispersant treatment	16	16	157.43	328.26
coral polyp · oil treatment	16	16	76.20	123.17
coral polyp · dispersant treatment	16	16	128.25	412.89
Polyp	10	10	21.92	53.70

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	-	69.13
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.65
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.72
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.76
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.45
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.47
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.44
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.26
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.46
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.77
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.34
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.10
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.57
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.54
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.78
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.64
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.61
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.97
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.69
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.82
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.54
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.79
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.00
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.74
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.27
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.51
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.99
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.45
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.78
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.28
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.22
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.69
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.10
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.72
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	138.58
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	129.15
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	118.98
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	107.04
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	102.93
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	94.06
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	90.20
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	75.02
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.43
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.02
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.82
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.09
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.89
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.05
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.72
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.82
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	328.26
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	294.60
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	245.13
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	201.09
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	191.28
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	170.07
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	140.74
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	132.59
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	130.11
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	127.86
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	120.09
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	101.80
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	96.08
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	92.71
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.58
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.94
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	123.17
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	119.50
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	107.84
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	100.35
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	93.04
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.43
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	75.13
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.11
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.43
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.06
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.69
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.17
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.58
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.62
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.73
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.33
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	412.89
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	206.06
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	172.25
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	159.13
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	147.14
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	146.47
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	139.37
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	111.12
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	104.66
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.32
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	83.38
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.33
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.88
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	75.89
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.97
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.07
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	53.70
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	32.88
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	30.39
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	26.03
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	21.96
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.92
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	13.69
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	11.18
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	10.21
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	5.25

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.