Gene detail

Detailed information of XP_032242336.2 in Nematostella vectensis

Genomic Location: NC_064037.1:11035622...11041628
NR annotation: XP_032242336.2, E3 ubiquitin-protein ligase RNF34 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032386445.2

CGGATGCCCTGTGGCATTCTAATTATTGTCGccgtgggtaccctgtgtgcaGATTGCTCTCCGTCACCCGTCACCGGATACATATCTGTGTATGATGTCTTTAGCAGCTTTAGTTATCAAAGGTTCTCATATTTTCCACTTATTAACCTCCAAAGTTTCTGTTTTTGTATTGAAATGGGGTCTGGAGGGCTGAATGGGGAGCTGAGGAACCAGTCGGATCAAGTTGATGCAATATTACGCTATCATTTTGCTGTACCTCACGACTCGAGATCAACACCCCAACACCAACGAACGACAACCGCAAATTTTCCCTCAACAAATCCTCATAATTCGACGACAAATCCAACGCCTGAATTCACTGAGATGGTGTGCTATTTGTGCTCGGTGAATTTCACCTTGTTCAAACGAAAAAGTACATGTCGAGGTTGCAAGAAGACACTCTGCAGTAACTGTTTCACACAAGGATTGAATGCTCGTGACCAATCACCACGTTGTATAACATGTCGAGCACTTGCAGCCCCATCAACACACAAAGACTTTCTACAATATCTGAAGATCAAAGACTTGCAGGACTTCTTAAGACTGAAAAACATTCCCATGTCCCAGTGTAAAGAAAAACGGGATTTGATTGAGTTAATACTACAATACTCACAGCCACGGAGGTATCCTGACTTTCCTAGAGGAACTCCTCATCCTCCGCCCCCTGTCACTCATGATCAAAGACAGGGGGGGACGCATCCTAACTCAAATAGTGGTCAAACAGCAAATAGAGTCAATAGAGCTGGGGAGAATAATGCATGTGAAACAAAAGAGGCAACTCGACGTACTATAGATGACATTACGGACATTGAACAAGTAGATAACCTGTCAGTCAAAGAACTAAAGCACATCCTTACGGCAAATTTTGTGGATTTCAAGGGATGTGTGGAAAAGGAAGAGCTGTTATCAAAAGTCCGTTTGCTATGGAAGTCAAGAAATTGTGAGAAACAGAAAGTTGAGAATGTGTCGGAGTCACTGGATGAGTCCTGTAAAGTGTGCATGGATAACCTGATCGACTGTGTCCTACTAGAGTGTGGGCACATGGTAGCCTGTATAAACTGCAGTAAACAGTTAGCAGAGTGCCCTATATGTAGGCAGAACATCTCACGAATTGTCAGGGTGTTCAAAGCTTAATGTTAATCATTCACAAATTACGACTTCTCCTAATTGATTAAGAGGGGGGCTAGAAAGGGGGGCTGCCAAAGAAAGAGCAATGTTCTCTTTCAGAAGAGTAGGGTACTTGCCGAAGAATTGTTATTCAATTCACAAGGAATCATCCTgtagatatatattttaaaatggaCCATGGATCACTTAAATGAAGGGGTCAAGAGCACAGGGGTCTCTGCCTCCCCTCTTCATCTGACCCCCCCTTTCTACAAGCACAATATTTGGTgtatttttttgggaaaatgAGAAAGGACTACAATTACCAGTATGTCTGCATGGTGAGACTGAATAGGCGAATGAGTTAATGTGTTGGTCTACTAGTAAAATTGGTGTAACTAAAATATGATccataacaaaaaatataatattgctTGCCACTATTCTTCATGTTTGGATCATAAGATGTTCGTAATTATGTAATACATTAGCCAGACCTCAGCTTCTGTAATATCGAtctgacttgcgtgacacatgGTTTGTAAGCTTTGAAACCCTGTGAGAATGAGATGTTCATCTCAGTAAGTGAATTAAATCTGCTTGAATCATGATGAATttcaatccatcctacaaCTAAAACAGCTcagttatattttttaaaatatcaaataaaacaggaaagttgtattttgaaaaatgatgcaagttttgaatattcaaaacaaaacaacattgcCATGTCAGATCTACAGACTACAGCACTTATTTTATTGCATGGTACTATTGTAGACCAGATAGCCTGAGTGAAAGGCCCTTTTATTATTCGCTGCGAAGAATATACTgggaagtgaaaaaaaaatttctctaaaacttttgaaaaataaaattgccttataCTCAGGGTATAGACCAAATGACTGAGATTTTTGTGTAAATACTGTATAATACACTTCTTGTATTACTTATATACACATGACTCAATAAATGTTTCTCagctttttgattggtcaaattTAATAGAACAATTGTATTATTTGCTTGAGACTAGTACTCATGATGCAGTGAAAGTCAATGACCAATAATGACCTGAGCAACGTTTTTTTGAGAAGATaagaaattaataataaaaataccaCTAAAGGCT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q969K3	E3 ubiquitin-protein ligase RNF34 OS=Homo sapiens OX=9606 GN=RNF34 PE=1 SV=1
Q5NVC7	E3 ubiquitin-protein ligase RNF34 OS=Pongo abelii OX=9601 GN=RNF34 PE=2 SV=2
Q5E9J6	E3 ubiquitin-protein ligase RNF34 OS=Bos taurus OX=9913 GN=RNF34 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008993 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13920 all species →	zf-C3HC4_3	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000306 all species →	Domain	FYVE zinc finger	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan
IPR036361 all species →	Homologous_superfamily	SAP domain superfamily	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR051728 all species →	Family	RING-FYVE domain-containing E3 ubiquitin-protein ligase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14879 all species →	CASPASE REGULATOR, RING FINGER DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0070936 all species →	Biological Process	protein K48-linked ubiquitination	Interproscan
GO:1902042 all species →	Biological Process	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	Interproscan
GO:2001271 all species →	Biological Process	obsolete negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis	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 XP_032242336.2.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of XP_032242336.2 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

42TPM > 0

16Conditions

22.9Max TPM

14.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	16.04	17.66
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	12.62	14.75
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	18.33	20.50
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	18.12	20.29
whole 6 week old aboral regenerate · regenerate uncut	3	3	13.03	16.00
whole 6 week old aboral regenerate · regenerate 4hpa	3	2	10.17	17.45
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	14.33	15.71
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	17.67	19.59
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	12.56	20.67
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	18.85	21.20
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	21.10	22.86
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	11.11	18.41
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	17.38	22.40
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	10.33	18.60
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	17.19	18.88
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	7.25	21.76

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	17.66
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	15.63
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	14.83
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	14.75
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	12.43
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	10.69
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	20.50
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	18.70
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	15.80
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	20.29
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	18.31
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	15.78
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	16.00
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	13.25
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	9.84
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	17.45
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	13.05
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	15.71
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	14.46
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	12.80
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	19.59
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	18.82
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	14.59
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	20.67
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	17.02
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	21.20
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	18.58
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	16.76
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	22.86
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	21.61
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	18.84
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	18.41
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	14.92
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	22.40
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	15.35
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	14.39
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	18.60
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	12.39
SRR6320868	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	18.88
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	18.60
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	14.11
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	21.76
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.