Gene detail

Detailed information of XP_032219019.2 in Nematostella vectensis

Genomic Location: NC_064039.1:7839983...7850940
NR annotation: XP_032219019.2, poly(U)-binding-splicing factor PUF60 isoform X2 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032363128.2

AATTCTACACAGGCTCTCAAACACgccaagaagaaaaaaatggcggctgtTGAATCGTTATCTTTGGCAAATCATCTAGGAGAAAATCAGCAAAACGGCGAGGTGATGGATTTGGGTGAAGAGAAACCAGCAGAACCCGCCTCGGTAGAGATCAATAGCAACACAGAAGGAGGACAGAGAAAGAGGAGGAAACGGGGATTTGATGTTGGCCCAGGAGATATGGAGATGGAGGAACAGACCCCGGATGATGGAACCAAGGGGACGCTACTCATCGGACCAGCCGCCGGGGGTATACAGCCGCGTGCCACAGAAAGCAAAAGAGCTCTTCCTTCCTTGACAATTATTCAAGAAGAGCTGCTCAAACGAGCCAAGCGATACGCCATGGAGCAGTCTGTACAACAGGTTCTAGCAAAGCAACAGGCCCTCCAAGCTCAACAAATGAATGCCTTGCAGACAGCAGCACAAAAACAGAGAGCACTGGCTCTTATGTGCAGAGTGTACGTTGGAAGTATAAATTTTGAACTGAGAGAAGAGCATATCAGAACAGCCTTCCATCCATTTGGTCCAATTAATAAGATTGATCTTTCTTGGGACCCTCTCAATATGAAACACAAGGGTTTTGCTTTTGTGGAATATGACCTTCCTGAGGCTGCCCAACTTGCTTTGGAGCAGATGAATGGTGTTCTGCTTGGAGGAAGAAATATCAAGGTTGGTCGGCCGAGCAATGTGCCTCAAGCGGCTCCACTTATAGAGCAGTTTGAGCAAGAAGCCAAGAAATATGCTAGGATTTACATTGCCTCTGTTCACCCAGACTTGCTAGAGGATGACATCAAAAGTGTTTTTGAAGCATTTGGCAAAGTGGTTCACTGCTCGCTATCAAAGGAACCCATGACAGGAAAGCACAAGGGATATGGCTTTATTGAATACGAGAACCAGCAGTCTGCAAATGATGCCATAGCTTCCATGAATCTGTTCGACTTGGGTGGACAGTTCTTGCGGGTTGGTAGAGCTATCACCCCACCCACTTCCTCTGCAATGGCAGCCATCAACACCACACCACCAGGAACTCTCCCTGCTGCGGCAGCTATAGCAGCAGCTGCAGTGTCTGCCAAGATTCAGGCAGAGGAGAGAGGCATTCCTCCAGAACTTGCACCAATTACGATCCCTGCAGTTACCACAGTCATAACATCAATGTTGCCTGGATCCGCTGGCTTGGTAGCTTTCCCTACTGTTGCTGTCACCTCCCTAGCGGCCGGGGTTATGCCCCAGCCTCTCATAACAGGCAGTCCAGGCTTAATACCAGCTCCTGCTACACCAATTGTCACTCCCATCGCTACCCCAGTCGTCACCACAGCAGCTCTACCAGTAACAACCACAGCTGCCATGatacaacaacagcaactTCAGCAACAGCAACTTCAGCAACAACAGCTTCTACAGCAACAAGAACTGctacagcagcaacaacaacagcaacaagaacaacaaagCCAGCGACAGGCCTCTGAAATTGCTCAGCAGCAAGCTGAGATTAAGGCAAAGATCGACGAAGAAACTCAACGCAAAATGGCTGAGGGAGGTAGCATCAGTCATGAGGAAAATATGTCTATTTCCGGAAGCAATGCCAGATATATGGTGATGCAAAAGCTATCTCGAAAAAGCGAGTCCAAGGTGATGGTGTTGCGTAATATGGTGGGCGTGGGAGACCTGGATGAAGACCTTGAGCATGAGGTTACTGATGAGTGCAGCAAGTTTGGTACAGTCAGTCGAGTGGTCATCTACAAGGAGAAGCAGGGGGAGGAGGAAGATGCGGAGGTCATAGTCAAGATCTTTGTCGAGTTCACTTCACCTGATGAAACCGACAAAGCCACAAGTAACTTAGATGGTCGATGGTTTGGCGGGCGAGCAGTCAAGGCCGAGGCTTACAATGAAGACAAGTTCCTGTCTGCAGACTTATCAGGCTAGCATTTACCTAGTCAAATCTGCTGAATCACTTGAAGAAACCGGATCTATTTGAAACATAGCCACGACATTGTGCATCAGAGGGCCAGATAGACATGCGTTAGCAGTTGTGAACACAAACACGACGAGTGCATCATGGGTTCACACAAATGACAGTAGGCTCGATTTCCATCCGAAAATTGATGTAAACCTCAGCTTAAGTCGAGCCTAATATTGCAGTCTATTTTAACTATTAGACATGTCAGTACAAACCATTCTTGTTCAATCTTTTAGCATGTACAGTGCTTTTCTAATGCAAGGAGGGTATTTCGAGCAGAGTCTAGTTACTTCATTAGTTATAATGTAAAATTTGTCAATGCGAATAAAAGGGTACCCGATG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3UEB3	Poly(U)-binding-splicing factor PUF60 OS=Mus musculus OX=10090 GN=Puf60 PE=1 SV=2
Q9WV25	Poly(U)-binding-splicing factor PUF60 OS=Rattus norvegicus OX=10116 GN=Puf60 PE=2 SV=2
Q2HJG2	Poly(U)-binding-splicing factor PUF60 OS=Bos taurus OX=9913 GN=PUF60 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003878 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006532 all species →	Family	Poly-U binding splicing factor, PUF60-like	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR003954 all species →	Domain	RNA recognition motif domain, eukaryote	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR034212 all species →	Domain	PUF60, RNA recognition motif 3	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR051974 all species →	Family	Poly(U)-binding-splicing regulator	Interproscan
IPR034209 all species →	Domain	PUF60, RNA recognition motif 1	Interproscan
IPR034211 all species →	Domain	PUF60, RNA recognition motif 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47330 all species →	POLY(U)-BINDING-SPLICING FACTOR PUF60-B-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000381 all species →	Biological Process	regulation of alternative mRNA splicing, via spliceosome	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000380 all species →	Biological Process	alternative mRNA splicing, via spliceosome	Interproscan
GO:0006376 all species →	Biological Process	mRNA splice site recognition	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 spliceosome	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
K12838	PUF60; poly(U)-binding-splicing factor PUF60	-	Spliceosome	ko03041	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_032219019.2 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

47TPM > 0

16Conditions

53.8Max TPM

36.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	36.62	38.71
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	29.48	38.83
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	34.65	37.65
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	36.01	40.16
whole 6 week old aboral regenerate · regenerate uncut	3	3	27.10	29.67
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	37.72	52.35
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	37.04	40.82
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	48.66	53.77
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	35.40	41.55
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	37.69	42.10
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	35.93	40.56
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	38.91	39.91
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	38.94	47.19
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	30.67	47.69
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	36.62	38.58
whole 6 week old aboral regenerate · regenerate 12hpa	3	3	35.89	43.29

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	38.71
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	37.40
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	33.74
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	38.83
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	26.64
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	22.96
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	37.65
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	33.30
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	33.00
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	40.16
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	35.77
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	32.08
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	29.67
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	27.07
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	24.57
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	52.35
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	31.14
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	29.66
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	40.82
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	35.41
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	34.89
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	53.77
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	49.98
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	42.22
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	41.55
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	39.67
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	24.98
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	42.10
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	39.27
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	31.72
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	40.56
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	34.39
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	32.86
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	39.91
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	38.54
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	38.28
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	47.19
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	34.84
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	34.78
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	47.69
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	44.33
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	38.58
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	35.71
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	35.56
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	43.29
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	38.60
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	25.78

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.