Gene detail

Detailed information of XP_032233004.2 in Nematostella vectensis

Genomic Location: NC_064039.1:8584466...8596633
NR annotation: XP_032233004.2, protein Mdm4 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032377113.2

TTCTCCCAAGTATTTAGATTCAGTCGCCGTATCGAACAGCATGTGCTAAGGTTCGAATGAGAGCGCTTTTGCGATGGGCTAGAAGGACGTTTGGTTGGAGAATGTAATGGAAGTGAAGGAGTGTGCCTTAGTAACACCAGCACGGCAAAATAGTGGATCGGTAGTAAGGCAACTGGCAAGGGCACTCAACGACAATGATACAGACCCATCAGACGGAGAGCAAGTGTTGGTTTCACCAGGCTCAAGTAGAAAGCTAAACAGGAAAAGAAAACGTGCAAATCTTACAGATGTGAGCTGTAGTAGCCTAAGTAGTGGAACATGTAGTCCTCAGAATATCCCTTGGTGCCTGGGCTTCATAGGCCGAACAGGATTTGAAAGTAATGAAGAGAAATCTGACTGCTCCAATCACAGCAAGCCATTTTGTGGTGTCAAAGGGTATGATACTGCAACAACTGCAGTCATAACAGACTCAGAGGATGATTTCTTCTTCCCAAATGAAGCCGAAGAGTTTCATAGATTTGAAGTTGAGTATGAGCCACCAGAAAGTAACAGTGAAGATGAAAaagatgacgacgacgatgatgaggATGAGCCCCAAATAATCATCTCGTCTGATGATGAAGACCCTGGTgccgatggtggtgatgaatATGATGAAGATGACATTGACACCGAGAGTGAGGTGGAGGATTCCTGGGAGTGTGACAAGTGTAAGACGATGAACCATCCAATGACAAGGCGCTGTGTTGTTTGCTGGGAAAACAGAGAAGATGAAGTTTGCTCAACACTTGTAAGGACAACCTCCGTGCCAGCTTATCGCCTTCCAGAAGCTTTTACATTTCCTGCTCCAGCCACTCCTACCTTGCATCGCAGCACAACCATTGGACAGCCAGTACATATTTACAATTCATCTACCGCTAACAAAGACAGCGTCACAACCCCCTCTGCATCTAGGTCACTTTTATTGACAGGcagtcaagcaggcgaagcGTCATCACGCTCGTCAAGCAGTTGCTCAAACACTCAACACTCCTGTGATAGCGGTATATGTATCTCGTCATGTGAAACAGACAATGAATCTACATTGCAAAATCCTACCCGTAATAAATCTGCATTGCAAAATCTACAAGATAATAAATCTGCATTGCAAAATCTAACAGACAATGAACCTGCTTTGCAAAATCCACTAGGCAATGAGTCTGCTCTACAAAACTTACTAGGCACTGAGTCTGCTCTACAAAACCCACTAGGCAGTGAGCCACCGATGGAAAATCCATCAGCCAACCAGTCTGCTTTACAAAATTCAACAGGAAATATGCCGGATAAGCCCAAACTTCAGAAACCACTTCCTGCAGTGGCAACATGTGCCCCAGAAACTGTTAAAAATAGTGAAGAAATGTGTGTTATTTGTCAATCAAGACCTCGGGATGCGAGTATCATTCATGGACGGTCTGGTCACCAAGTTTGCTGTATGCACTGTGCAGAAAAACTCAAGGCATACAAGAAAAAGTGCCCAGTATGCCGCAGGAAGATACACTTTGTGGTAAAGAATTTTCTGTAGATCCTCTCtagttttatagttttttttttattgctaatctttttattaaaagaaaacaGTACAAATGTTTACATTAAATCCTTGGTTGCAGTATTGCTCGTGACAAAGGAATTAAATTCAGgaaaattaatataaaaaataatatattaagatgtttttttgtttaggtACCTTTTTATAGAATTATATTTTTGGGAGTTTTGTACACTTCTTCATTTCAAGATATCTTCCCAAATAGTGAGCTAAAGCTGtctgtgtatgtgtgtgtatGAATGTCTGTCTGTGTGACTGCCTGTTTGTTGTTATGTCTACTTGTTTGTTTCTATGTAAATAGCTCTCTAATAACAACAGTATGGTTATAATGACAAATATTAGACCTTTATAAGGTTTCAAGTAAACCCTGCATTTAATATGAGGGTGTGTGTATGCGCTAGAGGGGTGCATATACATTAAACATTGCATGTAACAGCTTTTTTATGCAGTGATATGAGAAAGATTAGGGGTGACAGATCATATCTAAAGCCCCTCAAGAGCCAGTGCTAGCCACACCttagttattgttttcaaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O15151	Protein Mdm4 OS=Homo sapiens OX=9606 GN=MDM4 PE=1 SV=2
O42354	E3 ubiquitin-protein ligase Mdm2 OS=Danio rerio OX=7955 GN=mdm2 PE=1 SV=1
Q2HJ21	Protein Mdm4 OS=Bos taurus OX=9913 GN=MDM4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006630 (this species only) · gene tree & orthology

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
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR036443 all species →	Homologous_superfamily	Zinc finger, RanBP2-type superfamily	Interproscan
IPR001876 all species →	Domain	Zinc finger, RanBP2-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46858 all species →	OS05G0521000 PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0007049 all species →	Biological Process	cell cycle	Interproscan
GO:0010468 all species →	Biological Process	regulation of gene expression	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0043066 all species →	Biological Process	negative regulation of apoptotic process	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

No KEGG orthology assignment for XP_032233004.2.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_032233004.2 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

34.6Max TPM

13.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	16.86	21.42
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	11.49	20.70
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	19.86	25.92
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	13.55	19.84
whole 6 week old aboral regenerate · regenerate uncut	3	3	11.33	14.21
whole 6 week old aboral regenerate · regenerate 4hpa	3	2	9.87	19.20
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	17.86	21.64
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	14.80	19.64
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	8.66	15.35
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	12.61	13.13
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	11.21	13.55
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	20.78	34.56
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	15.26	19.43
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	13.06	19.64
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	9.68	16.95
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	4.56	13.68

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	21.42
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	15.93
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	13.22
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	20.70
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	8.21
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	5.55
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	25.92
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	18.14
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	15.52
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	19.84
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	11.63
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	9.19
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	14.21
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	12.48
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	7.32
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	19.20
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	10.41
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	21.64
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	20.05
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	11.89
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	19.64
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	14.87
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	9.90
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	15.35
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	10.62
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	13.13
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	13.07
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	11.63
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	13.55
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	11.43
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	8.67
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	34.56
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	13.98
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	13.81
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	19.43
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	14.21
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	12.15
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	19.64
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	19.56
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	16.95
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	12.10
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	13.68
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.