Gene detail

Detailed information of XP_001624062.3 in Nematostella vectensis

Genomic Location: NC_064038.1:2280825...2290215
NR annotation: XP_001624062.3, secretory carrier-associated membrane protein 2 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_001624012.3

CGCATGCGCAGCAGTGATCTCTACACGTCCGAAGGCTAGTGTCGCTTTATAATCTCGTCTCCCTTGAAAACACTCAGTTTTTCCAACAGAAAAAATTCTAATCGTCTCACTTTATTCCTGTCAATATGGCTGAAGGTGGATACGGAGATCCAGAAAATCCTTTTGCGGATCCTTCTGTGACTGACATGACGAGCGGCGCTTCTCGCGGCCTTGGAGATTTCAATCCTTTCGCGGAGCAAGACACTTCTTCTGGCCTCACGACCAAGCCCTCTCCAACGACAACAGCAGCCCCTCCTCCTCAGCTACCACCACAGCCCCAGGCTAAGACACAGCCAAGCCAACCAGCCGTGCTTCAGACACATCAAGATCCTCCGCCTTATGTGATAGAAAATGAGCAAGAGAATCTAAGGAAGAGACAAGAGGATTTGGAGCGAAAGGCAGCTGAATTGCAAAGAAAAGAGCAAGAACTACAGCGCATGCAGTATTCAGGCTACAGAGAAAACAACTTCCCGCCCCTGCCTGAATGGTTTAAGTTAAAACCGTGTTTCTACCATGACATTCAGGTGGATATCCCCATTGAGTACCAGAAATTGTGCCGGTTCCTCTTCATTAGATGGCAAGCTTACAGCTTTGTGATGTTTTACAATTTTATCGTTGCATTGGCATTGTTAATCACGGCTGCTACAGGCAACCACAATGAAGGGAAAACATTTGGTCTTTCTATCCTCTACCTGGTCTGGAATGTCCCAGCCAGTTTTCTATGCTGGTATAGGCCAGCCTACAAAGCACTAAAgaATGACAGTTCATTTAGCTACATCATCTTCTTCCTGATTTTTTTCCTGCACATATCCATCAATATTTACTACACGCTGGGGATCCCTGGTGGGGGGTCATGTGGGTTTATAACTGCCACAGATACGTGGCATGGCACCAAcaaggcagtatccatcatgATGTTTATTTGCGCTGCAATGCTGTTGGCCGGAGTGGGCATTGACTGTATTCTAATCGTCAAAGTCCATCGGATATACCGCCAAGCTGGTGCCAGTCTTGAGAAGGCGCAAGGCGAGTTCGCCAAGGGCGTGGCCACCAACCCTCATGTCCAGACAGCAGCTGCCGCTGGGGTCCGCAATGCAATGTCCAACCAGAAATAAATCACCCATCTCCCACATGGAAAAGGATAGAGGGAACAGGCTACCCTCCGTTCAGAAACAGTGCATCAAGAAAGTGTCTTCTCCCTGTCCTTTTAAGGATATTGGACTCAGGGCGGAAGCTTCCCTAGCATGACTAAGTACATAAGAAGGCAAACCTCTTTTTAGAGTCTGTCCAGCAGTTATTTTGAACGGAGGACTCGTAGGTATATGGAATTTTGAAGACATGCCAAACAAACTGGCGTCTCAAAGACATTTAATTTGTGCATTCTCTGACACTTGACGTAAGTTTTGATTGTTAAACTTTTCCTGTAATGCTGTAACCAAGGAAATACTGGGCCTAGTACACTAGAAATAGCAAACCAAGCATTTGTTAAATTTGTATGTTTATTCTCAGGATTCGTGCTTTGATACACTTTGTGAAAACATTTGCATTTAATGACTGTGTTATTGAATGATACGTTTGTTCCTAACTACCAGTGTCCTTATTAATGACGCTCACTACCGTGGCCGAATACTAATGGTCttcttattttgggaaatttTCGCCAAAACGTTCAATCAGACATTTTGTTGATTGGACATTTTCAATCAATACCTTTATCGTACCCTTATTGGCTAACATTCTAAAGACTTTTTTaaggtggtcacggtagcttGCGTAAGATAGTAACGTGAGGAAATATGTTGGCTATAACCCCTTAAAATTATTGCTAGACCATTTCATCTAAAGCGCATTCAGTATCTATTGGACGCATATTTCATAATATTCCGCGCATTTGTTTCACTTTTTCCACATCTATATTGGCTCTGGAAAGTATTAATTATTAACGTCTTGAAAAGAGAATTGTCTATTTTGCGATTGAgattaatataattttttgtcaactttgttaaaaggattttttttaaatacggCTATGTATGGTCTTATGGGGTTTCGTTGCGAAAAGTAATATACTTCTGCGTGCAAAATTTCTTGAATGAGCTTATGCCAGTATATACCTGTCCATGTTAAAGAacataaatttattttgtaagGGATGGAAAAGGTTGTTAATACATTATAGTAATTGACTTTGGATTAGGAAATAAATTTATAATCGACGTA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O15127	Secretory carrier-associated membrane protein 2 OS=Homo sapiens OX=9606 GN=SCAMP2 PE=1 SV=2
Q9ERN0	Secretory carrier-associated membrane protein 2 OS=Mus musculus OX=10090 GN=Scamp2 PE=1 SV=1
Q8K021	Secretory carrier-associated membrane protein 1 OS=Mus musculus OX=10090 GN=Scamp1 PE=1 SV=1

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 XP_001624062.3 across 48 RNA-seq samples of Nematostella vectensis. 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.

48Samples

46TPM > 0

16Conditions

70.1Max TPM

32.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	32.14	35.29
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	25.88	32.26
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	31.42	39.34
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	36.62	41.88
whole 6 week old aboral regenerate · regenerate uncut	3	3	24.43	29.34
whole 6 week old aboral regenerate · regenerate 4hpa	3	2	18.72	33.42
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	34.27	37.55
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	34.61	40.87
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	38.16	43.57
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	37.96	38.99
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	33.36	40.25
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	39.07	41.52
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	35.02	35.50
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	49.90	70.09
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	27.53	30.86
whole 6 week old aboral regenerate · regenerate 12hpa	3	2	19.35	39.07

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	35.29
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	33.78
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	27.35
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	32.26
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	22.86
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	22.52
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	39.34
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	27.65
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	27.28
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	41.88
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	34.85
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	33.14
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	29.34
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	22.33
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	21.62
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	33.42
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	22.74
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	37.55
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	35.31
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	29.94
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	40.87
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	31.53
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	31.42
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	43.57
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	37.04
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	33.85
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	38.99
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	37.50
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	37.41
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	40.25
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	30.18
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	29.64
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	41.52
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	40.44
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	35.25
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	35.50
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	35.30
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	34.25
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	70.09
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	41.28
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	38.33
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	30.86
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	29.18
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	22.56
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	39.07
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	18.99
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00

Source: CnidoSite RNA-seq expression matrices (NVECT_TPM, StringTie quantification over 48 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.