Gene detail

Detailed information of XP_048590318.1 in Nematostella vectensis

Genomic Location: NC_064044.1:4382766...4403450
NR annotation: XP_048590318.1, probable ubiquitin carboxyl-terminal hydrolase MINDY-4 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_048734361.1

CCATGCTTCAAGTCAGCAGCATCCCCCATGGCAACTGTAACTGAATCAGTTTAGGAACGAAATACAGTCtcaaaaatatcaatttttgCCAAAATTTATCTATCAGTCGCACTTCTTTAGAGCCCTGAGATCATGTGCATCATTTTGGATTATTGTTTATGATTATAGCAATGTCTTAATGTCGAGATCAATGGAGTTTGTGCAGCCCGGGAGATTAACTCCAAATAACGCAAAAGCGAAGTGATTACAAATTTTATCATGAGTGATGTAGAATCGCTGACGGCTTCTCTAGTAAGAGAATATCTCAGTAGAAAGGGGCTCAGGAGTACACTAAAAGTCATGGACCAGGAAATTCCAAGAACTGATAACAGTATCAGCAATCGTGCACAACTCGCCAAGGAGATCCACATCGAAAAACTTatgaagaaaaacaaaGAGCAAGCTGTTGCATTTCGTACAATGCTGGAGGTTATTGTGCAATATTTCAAAGAGAAAGGCGCTCCTTCTCTTTCTACAAGGCCAGGCGCACCTGAGCCTGCTCTACCACGGTCAGCAGCAATTGAGCACACAGCACTGAGATCAGACCAGCCTGCACTGAGCATCAAACAAGCACAGCCCTCAAACAAGGAAAGGAAGTCAAGCATAGAGAAATCAAAGAAAGCTGAAACAGTAGTGGAATCATCAGATAAACCAGCTGATGACTCCCATGATTATAGCGATCTTCTAAAACGACTAGAGAAATCGGAGACACCAGCCAGAAAGTCTGAGCTCTCTGAACCCCTTGGCTCACATAAATCACTGCACCTCAACCAGAAACTTGGCTCAGAAAAACAAGCTGAAAAGCCAATGAGGCCCAAGTCTCATCGCAGCCGTACCAAAAGTGGTGGTGGGCTAGGCGGACCGGTGATAAGCTCCGGACTGGCAGGCTTAGGGGACAAGAGGATAAAACACAAACGGAACCAATCTTCTGAACTCAATGTTACTGGACACAGTTTTAGCACTGAGAAGGTTGTACTTGATGACGATAAAGCCAGTGATGGATTGTTCAAACCTGATGATATATTTAATAAGCCACCTGAAACGTTTATAGAGGCAAAGAAGGACATTCCTGCAACCTTCCTACAGCACGACACTCTAGATGGCTTTCAGAGGAGTGGTATACCTTCAGCCACTACATTGGATAAACTAAAaAAATCGTCTTCTGGTTCTACTTTTATTCAGAAAGATGAGTTAGTTTTTgaagatgttgatgatgaattGGACCAGGATCTAGGCCAGTTGTCTCTGGGACCAACCGCTTTATCTGCAGACTTTGAGAGTAAAGCTATTTCTCTAGAGAAGGCCATGGCTCTCAAGAACCTGATATTTGGCACAGCGACAGCTTGCTTTAACTCGGAGTGGAAGCAGCAGGGTTTTGGCTTCTGTGATCTGTATGGTCTCGAGTTTGGCATAGTACAGTACAAGGGTGGACCCTGTGGTGTGCTAGCAGTAGTTCAAGGATTTGTACTGAAACATCTCCTCtttcaagaaaataataaaagtaacaaaaaAATTCTCCAGCCATCATCACGTGAGAGATCGCGGGCGCTGGCGTCCGCTATCACTGAGATCCTATGGCAAGCTGGGGATAGCAAAACAGCAACAGTTGCTCTGCCTACAGGGATGGCAAACTCTAATTTTATCGGAGCTGGCAGATACAAACCTGACCAATTAACTGAAAATCTGGTGTTACGCTCATTCAAGTCGTCCGAGAGTCTTCACAGCTTTGTCACCCAACAGATCTCCCAGGTTGGCGGGAACTTTAAGACCCCAAGGCTTCCCATCTGGGTAGTATGCAGCGAAAGTCACTTTAGCGTGCTGTTCTCTCTAGACAAAGACTTGCTCACTGACTGGAAACGAAGTAAGAAGTTTGATCTGTATTATTATGACGGTCTAGCCAGACAGGATGAGGAGATTAGATTAACAGTTGACACAACGCAAGAGTGCCCAGAATATGACGAGGGAGACCTTGTGCCACCACTAGAACTCGTTATTAGGACAAGATGGAAAAAGGCAACAGTCTCGTGGAATGGCTCAGATCCTATATTATAATCTCATTTAGACATCATATCTGAAAATATGTACATTGAGATGGCCGGCTCCTAAGCATGAAAGGGTCAATAATACGACTGGTAGAATGTATAATTTTATGTAAAATACTCAATTGATCATGTTGAGACAAACACATGTTTAGgcattttaaaatttaaatattGTTGTAACATTTGGGCAAACAATTACATTGtccaattttatttattgtcattCATGTTAAATAATATCATGTACAGCAATGTATGTAATAAACGCAGGGGTAACCCTTTCAATGAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3UQI9	Probable ubiquitin carboxyl-terminal hydrolase MINDY-4 OS=Mus musculus OX=10090 GN=Mindy4 PE=1 SV=1
Q5RF72	Probable ubiquitin carboxyl-terminal hydrolase MINDY-4 OS=Pongo abelii OX=9601 GN=MINDY4 PE=2 SV=1
Q4G0A6	Probable ubiquitin carboxyl-terminal hydrolase MINDY-4 OS=Homo sapiens OX=9606 GN=MINDY4 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001667 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13898 all species →	MINDY-3_4_CD	Deubiquitinating enzyme MINDY-3/4, conserved domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039785 all species →	Family	Deubiquitinating enzyme MINDY-3/4	Interproscan
IPR025257 all species →	Domain	Deubiquitinating enzyme MINDY-3/4, conserved domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12473 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004843 all species →	Molecular Function	cysteine-type deubiquitinase activity	Interproscan
GO:0071108 all species →	Biological Process	protein K48-linked deubiquitination	Interproscan
GO:1990380 all species →	Molecular Function	K48-linked deubiquitinase 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
K22647	MINDY3_4; ubiquitin carboxyl-terminal hydrolase MINDY-3/4	EC:3.4.19.12	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_048590318.1 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

44TPM > 0

16Conditions

13.7Max TPM

3.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	4.06	4.64
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	3.26	4.38
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	3.90	4.65
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	3.83	4.66
whole 6 week old aboral regenerate · regenerate uncut	3	3	3.04	3.43
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	3.53	4.43
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	4.47	5.10
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	2.55	2.79
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	1.78	3.38
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	2.31	2.84
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	2.77	2.93
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	3.09	3.76
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	3.67	4.38
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	7.10	13.66
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	2.75	4.25
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	0.82	2.45

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	4.64
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	4.09
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	3.46
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	4.38
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	2.91
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	2.50
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	4.65
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	4.03
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.02
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	4.66
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	3.63
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	3.20
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.43
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.05
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	2.62
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	4.43
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	3.32
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	2.84
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	5.10
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	4.17
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	4.14
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	2.79
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	2.65
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	2.21
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	3.38
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	1.96
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	2.84
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	2.17
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	1.94
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	2.93
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	2.72
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	2.66
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	3.76
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	3.29
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	2.24
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	4.38
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	4.00
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	2.62
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	13.66
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	4.56
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	3.08
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	4.25
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	3.99
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	2.45
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.