Gene detail

Detailed information of XP_001637963.2 in Nematostella vectensis

Genomic Location: NC_064035.1:6973937...6979729
NR annotation: XP_001637963.2, pre-mRNA-splicing factor CWC25 homolog isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_001637913.3

GGTAGTTACCGCTGTCTAAACTGCTGTTTTGACGAACAACAAAAATTTAGTCGTAACTGAACGTCAATTTAGAATGGGTGGCGGAGATTTAaatttgaaaaAGAGTTGGCACCCGCAAACACTTCGAAATGTCGAACGTGTATGGAAAGCTGAACAGAAAGCTGAGGCGGAGAGCAAAAAGATCGAGCAACTTCGCCGTGAATTATTGGAGGAAAAGGCTCGAGAAGAGATGCAGAGACATGCAGTACAACAGGGGATATCAAAAAAAAAATCTGAGCGCCTAGACTGGATGTACTCTGCTCCAGGACAGATCAACAGAGAAGAATATCTCCTAGGAAAACCCATTGATAAACAAGTGGACCCCTTGGCTAAGGAAGATGAGGGCCTTGGCTCTCTCCCCGGGGCTTCTTTCACTGGTGACTCCAGTGCTAACAATGCATCAGACCTCGCAGCTAAAGTGAGAGATGATCCCTTGTTCATGatcaagaaaaaggaagatgaaaagaaaaaagagctCCTCCAGAACCCTGTAAAAATGAAGCAACTCAAAGAAATGCTAGAAGCAAATGTAGGAAAATCCAAAAAGAAGAAAGGAAAAAAGgacaagaagaagaaaaaggaaaaaagaggGGGGCCAAGTAGACACAATAATGCCTCTGAGGACAGTTTCGATTCTGGTGAggaggaaaaaagaaataagaacAGTGCAAGAAAGATGTCACCCATAAATGGACACAAGAGTTCTAGAAAAAGTCGCCATAAATCAGACAAAAAGGAGAGGGCTTCTCGGAAAAGGAGACATTCCAGGTCTGAGTCTCCACCAGTCAGACATCCATCAGGATCACAAAGTGGGGACAGACAAAGAGAAAGAAGATTGCACAAACACTCATCTCCATCCATCTCACCATCCCCTCCAAGAAGACAAAAATATTCGAATGGACAGTCAGACAGAAAAGGCAAACACAGACACAGGGATTCCTCTTCACCCTCACCACCAAGACACAGGTCAAGATCGCCATTTAGGAATggaaacaaaagaaagggtTTTCCTACCCATCGAAACAAACAACGATCTCGGTCAGTTTCCCCTGTACAATCAGGACAAGCATCACAAGTAATGAAGAGACGTGTCCCATCTCCAAGGGCGGATCGGCGCCAGAGAGGATCCGCAATGACGAAAAAAATGGATCCTGAAGAGCTTGAAAGACGTCGACAAGAGATGCTATCAAACGCCCAGTGGCGAAACGAACAGAGGGTGGAGAACGTGACCAAGTACAAGGAAGAAGCAAAGAAAGAGGCCGAGGCAGAGGGGAAGAATTCTAAGAAAAGTGCAGACTTTTTGAGTTCCATGAAAGTTCAGTCTTTCTCGTCCCAGTCTACCGCTTCAGTCTCCGACAGAATCAAAAGAAATATCAACTCCGTTCAGCGTACAGCTCACGCTCTTGACACCTTCCTCAAGAAGTGAGATTATTTGCATCAAGTGAACTTATATCACCTGCACCCATTATACAAGCGCACGTCAAGTGTCCAATTGGCCCCCCACGAACCTGCTAGCCTGCTAGCTAGGTTCTCCGGTCTGTTTATGTACCCGCGTGGGAGCTGGTCATGAAGGCCTTAGACAAACCCTGATATCTCTATCGCGCATGCGTTCCATTGTCCGATCGCTGCTGGATGGGACTAGGTACAACAGATCCTCGCGTTGAGGGGCAGGGCATCAGGGACCAGATATGACCCCACAACGAACTAGGGCATCAGAGAAATAGGAGCAAAATATATGCCCCCTTATAAAAACAACTATGATATGTTTCCATAGGGAGTCAGGGAAATAGGAACAACAAATATGATCCCCGTGTTGAGAGGCATGGTATCAGAGGCCATCAACAACAGATGTGATCCCATAAGAACTAAGATAATATGATGCCATCGGGAGTCAGGGGGTCAGGGAAACAGGAACAATATAGATATGATCCCCACGTCGAGGACGTCAGGGACCTTAGAACAATGGATATGATCCTCGCGTCGAAAATACTGACTGGAAGGAGAGACAGTAGAAATCAGCGCGAAGACATACGCGGAAATGAAATGAATTGAACGGAACGGTTCCTTTTCTTCCTCCTCGGTCTTCTCGCTGTTTGATTATCAAACGCTTGTAAGCTTGCACGTCTTACCACTTTCTCTGTCTTGATTCCTTTGCTTTATAACTGGCTTGAGTAACGTCGAAATTTGAGAGGGCCCTAGGGGATTAAACTGTTGTTTCATAGAAGAGTTAAGATCCTGGAATGAGATCGTCCGTCGTGAGGCTGTCAAAAAACAAGGAACACAATTGTATATACGGTACAGCTGTAAATAATAgagttttagaaaaaaaaacttattttatTCCCGTTGTATTTTCGTACAAAGAGTATAAGATTGAGAATTTGGACCATAAAGAGCCGAACCAGGagtataatatttatttattaacagGACGTGATGAGTTTATGGTATCACCTTAGGTCTATTATCTATGTATTATGTATTATCTTTTTATTATGTATATCTTTTTATACTTTTCGTATATTTACATAGTGTATAATATTTTGTAAATGGAACTATATGAACTGATATGAACTCATATGAACTTACTTGTATCATTAAGAGTGATAAATCTGTTAatgattttattatataaaattgGTGTAATATTCATTAAGCGGTCAACTCCTATTTAGCCActtttcaaaattaaaaatattgcttttcGCTACCTAAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9NXE8	Pre-mRNA-splicing factor CWC25 homolog OS=Homo sapiens OX=9606 GN=CWC25 PE=1 SV=1
Q9DBF7	Pre-mRNA-splicing factor CWC25 homolog OS=Mus musculus OX=10090 GN=Cwc25 PE=2 SV=2
P0CM99	Pre-mRNA-splicing factor CWC25 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) OX=283643 GN=CWC25 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006854 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10197 all species →	Cir_N	N-terminal domain of CBF1 interacting co-repressor CIR	Domain	Interproscan
PF12542 all species →	CWC25	Pre-mRNA splicing factor	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051376 all species →	Family	Pre-mRNA-splicing factor CWC25	Interproscan
IPR019339 all species →	Domain	CBF1-interacting co-repressor CIR, N-terminal domain	Interproscan
IPR022209 all species →	Family	Pre-mRNA splicing factor	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16196 all species →	CELL CYCLE CONTROL PROTEIN CWF25	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005684 all species →	Cellular Component	U2-type spliceosomal complex	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_001637963.2.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_001637963.2 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

41TPM > 0

16Conditions

15.1Max TPM

8.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	10.56	13.56
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	7.39	9.52
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	8.11	9.31
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	9.80	11.16
whole 6 week old aboral regenerate · regenerate uncut	3	3	8.37	9.51
whole 6 week old aboral regenerate · regenerate 4hpa	3	2	6.46	9.95
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	5.96	10.10
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	11.44	15.14
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	8.15	14.58
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	8.86	13.50
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	11.20	13.20
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	11.08	13.97
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	10.05	12.17
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	9.04	14.49
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	10.42	12.46
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	4.39	13.18

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	13.56
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	10.21
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	7.90
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	9.52
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	6.90
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	5.76
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	9.31
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	8.31
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	6.71
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	11.16
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	9.54
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	8.71
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	9.51
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	8.47
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	7.11
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	9.95
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	9.44
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	10.10
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	7.78
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	15.14
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	10.82
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	8.36
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	14.58
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	9.86
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	13.50
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	13.08
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	13.20
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	10.96
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	9.43
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	13.97
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	10.30
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	8.96
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	12.17
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	9.57
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	8.41
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	14.49
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	12.62
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	12.46
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	10.04
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	8.76
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	13.18
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.