Gene detail

Detailed information of XP_001635686.2 in Nematostella vectensis

Genomic Location: NC_064035.1:2447093...2461151
NR annotation: XP_001635686.2, E3 ubiquitin-protein ligase ZSWIM2 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_001635636.3

TGTCCCTAGTCTCTCGCGCCACTCAGTTGCCAAGGAAAATGAAAACAACGTTCGACTTCATAGACTTATAGAAAATAACGATTTCTAACTTTTCAATACCAAACTCTTCGAGGAATTTCTTCTAGAAATGGCAAGAAGGGTTCCATGGAGAAGGAATTGCCCCGATGTTGTAAGCTATCGCATCGAACAAGCAAATCAAGCGAGGATTTACCTGCTCCGTGAGACCGGACCGACTGGGTTCTTGTTGAAGCAGGATGGGATAGACAAAAAATTCAAAGTTTTTCTTGGAGATTTGCACTCCTGCACTTGTAGCACGTTCATGAAGGAGAAAGAATTGTGCATTCACATTCTCTGggtttTGCTGAAGAAATTTAGGGTACCCAAAGAGAATGAAGtgGTTTTCCAGTTGTCCTTAGTTGAGAGGGAAATTAATGAGGTTATGAGAGGGGCATATGTTCCAGCCCAGAGAGCAGCAGAACCCAAATctgaaaacacacacacagacAACCGTgataaaatgaaacaaaaagaaatatcAGAGGAAGATGTTTGCCCTATTTGCCAAGATGAGCTGCTGGACAAGTGTGAGCCTCTGACTTATTGCAAGTACGGCTGTGGTAACAGTGTCCATATAAAGTGTATGAAAGTTTGGGCAGAGCACCAGAGGTCAACTGGAGAAAAAATCACCAAGTGTCCACTTTGCAGAGTTGATTTTGGGACCTTTCAGGAACTGATGGACGAGTTTAACAAGTCATCCAGGAAAAATACACGATCTGAGAGGCATGATGTTCACTTGGGGGCGTCTTGTAATAAGTGCAGAGTTTGCCCGATTACTGGAAAATGCTATAGGTGTGTGATCTGCTCAGATTATCACCTGTGTCACCCGTGCTTTTTAACAGACCATCACATGCAGCACTCATTCCAATTTAGACAAAATGCAAGTCAGCGCTGGAGACCCGCATCCAGAATTACTCCACTCCCAAGCGCAGTGATAGAGAGCCTTCAAACACGCGAAATAACAGACAATGACTACGACCTGTTGTTACAGCTTGATAGACCCTTGGCAGAGCAAGAGGGCGTGtcaggtcacatgatcagtCGGCTCCCTGTGGACGTACTAAGAGAAGGTCATCCTCTCCTCGCAAGAGGTTCTACCTGTGGTGTCTGCCTGAGCGCCTACCACCCTTTGCAGTACGTCCGTAAATTGCAGTGCCGGCACGTCTTTCATCGTGATTGCATAGACTCCTGGCTCGCTACACAGTCGATCTGCCCCGTGGATGGACAAACAGTGGGTGTGTCGTACATGGGCGTGGCTCACACAGAGGTAGCACCCCCTGTTATCAACAGTGCAGTTCAGGGTGCTGCTAGAGGCCGACTTCTCAATCGGAGGCGTGAGACAAGGAAACAACTCGACCCTGGGAACACACCTGTCACGCTACCTAGCAGCTTTGAGCTGAGTGGGTCAGGAATTCTTGCCCGTGACAGAAGCAGGGACAGCAGTCCCAGTGAAAGTGGGCGTGGCCGAGCTCTTTTGGTTGATTGTTCTCCTAGCAACCTTATTGAAGCAAACAGGCTACGGAACCACGAGCCCGCGATGCGTAACCCATTACAAATCAACGGGAAACCACCATGGGCGCCAAATACTACAAACACACGTGGGAGCCAAAGTAGTGACTCACGAAAGAGAACTCCTGCCAGAGGTGGAGCACAGCAAAAACGAAAAACGTTGAGCCGTGACCATCGAAACAATTCTGTCGATGACATTTTTCTGTCTGCAACTGGACGAGCAGTATCCATAGAGAACTTGTCCCGCGACACTCTAGCTAGCTCCTCAACCGTCAAGCCCAAAGGACATTTGATTAAAGGGAAACTAGCGTGCAAAGTGTCTGATTACTCTCACTCAGACTCTGAACTGTCGACTGGCTCTGGTTTAGTAGCACTCGCGATACAGATGCCAGCCGTGGACAGATAGCAAAGTATGGGAGAATCTGGGAAAGGATAGAGGCAACACAAGTGGTAGACAAAGGGGAAGATCTACCAGTTGTGAAGGAAGAGTTGGTACGAGTGCGGTAGGGAAGGCAGAAGTTGTCTTTTAGGGTTAGAGTTTGCATGAAACTTTTTCACTGCAGCACTAAACTCACATTTTCACAAATCACTTAATGTGAAGCTTAGCTGGGTTAGCCACGAGTTACTGTGTGTTGGTGCTGAGGGGATATAACATCCATGGTGTTCCAATTGCGCTGTAGAGTGttttacaattaaaaaaagaataaaccaGG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8NEG5	E3 ubiquitin-protein ligase ZSWIM2 OS=Homo sapiens OX=9606 GN=ZSWIM2 PE=1 SV=2
Q9D9X6	E3 ubiquitin-protein ligase Zswim2 OS=Mus musculus OX=10090 GN=Zswim2 PE=1 SV=1
Q9SLC3	E3 ubiquitin-protein ligase ATL41 OS=Arabidopsis thaliana OX=3702 GN=ATL41 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007859 (this species only)
Ubiquitin family	E3\|E3 activity RING\|PHD · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13639 all species →	zf-RING_2	Ring finger domain	Domain	Interproscan
PF04434 all species →	SWIM	SWIM zinc finger	Domain	Interproscan
PF00569 all species →	ZZ	Zinc finger, ZZ type	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000433 all species →	Domain	Zinc finger, ZZ-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR007527 all species →	Domain	Zinc finger, SWIM-type	Interproscan
IPR043145 all species →	Homologous_superfamily	Zinc finger, ZZ-type superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR039903 all species →	Family	E3 ubiquitin-protein ligase Zswim2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21540 all species →	RING FINGER AND SWIM DOMAIN-CONTAINING PROTEIN 2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	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
K15716	ZSWIM2; E3 ubiquitin-protein ligase ZSWIM2	EC:2.3.2.27	Ubiquitin system	ko04121	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_001635686.2 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

36TPM > 0

16Conditions

11.2Max TPM

2.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	2	1.92	3.20
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	2.82	3.07
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	2.22	2.51
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	6.48	7.20
whole 6 week old aboral regenerate · regenerate uncut	3	3	5.72	11.16
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	1.45	4.36
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	2.47	4.01
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	2.00	2.36
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	2.48	4.36
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	3.64	8.18
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	3.33	5.38
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	2.15	3.26
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	3.19	3.95
whole 6 week old aboral regenerate · regenerate 48hpa	3	1	0.99	2.97
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	2.27	3.56
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	1.47	4.42

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	3.20
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	2.55
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	3.07
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	2.89
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	2.51
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	2.51
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	2.19
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	1.97
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	7.20
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	6.58
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	5.65
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	11.16
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.45
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	2.56
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	4.36
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	4.01
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	3.41
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	2.36
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	2.01
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	1.64
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	4.36
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	3.09
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	8.18
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	2.75
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	5.38
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	2.71
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	1.91
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	3.26
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	3.19
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	3.95
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	3.25
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	2.38
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	2.97
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	3.56
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	3.27
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	4.42
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00
SRR6320879	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.