Gene detail

Detailed information of XP_001633895.2 in Nematostella vectensis

Genomic Location: NC_064036.1:6964643...6968547
NR annotation: XP_001633895.2, caspase-3 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_001633845.3

TTCATCTTATCGGGGATGACGTCACGTTCGCCTTATAATTCCATTGAAGAGAAGCTTTCCAAATCAGCAGCGAACAAGCAAAACACTGTTAAGGTTAAGTTTGATATTTGTAGCGTTAATATGGATCCCGCACACAGAAGGACCCTCCGAACACATAGACTAGATCTTATTAAAGATCTTGAAGCCGATAAAGTCGCTTCAACGCTTTATGGAGTTGGAATTTTAGACGAAACGGACTTAGAAGATATAAAAGCTGCCAAACCATCGCAGGAAAAAGCTGAAATTCTACTGGATAAACTGCCAAAGAGGGGCCCAGATGCCTTTAGCAAGTTTTGCGATGCCTTGGAGGATATCTCACCACATCTTGCATCCTATTTGAGACCCTCTCAAACGAAAGATTCTGGGAAGCTATCAGGAGATGTAGAAGATGGTGCCGCCCAGGGTCCTATTGAATCTGTTGATGGTGGGAATGCAGAAGGCGGTGGATTGACTGTTGATGGTGGGCTGAATATATTTGGCAGCAGCTCCAAGTCATCTAGCCCTTCGGGAGACCTTCATATTTATAAGATGGACAAGACACCAAGGGGTGTAGCAGTCATTATAAACAACAAAGATTTCCTTCCTGCATCAGGCATGCATCGGTACCCTCGCAATGGCACCAATGTAGACAGAGATTCCCTGGAAAAAACTTTTAAGGCCTTGCAATTTGATGTTGAAGTTCACAACAATAAAACGACCTATGAGACTAACAGAATTATCAAGGAACTTGGTCAGAGGAGTTATTCTAACTACAATGCTATGATCTTTGCCATTCTTACCCATGGTGAGGAAGGGATACTCTACACCACTGATGGAACGATAGAGATTCGAAGCATGATGAAGGCATTCAAAGGTGACAACCTTGTTGGCAAGCCTAAAATCTTTATCTTCCAAGCCTGCCAAGGACATGAGTATATGGATGGTAAAGATGCCACCGATGCCGGCCCCGAGGATGCCAATCGTGTTCAAGTCCCAGTGGAGGCAGACTTCCTGTATGCCTACTCCACCGTGCCAGGGTATTACTCATGGCGTAATTCTGTTAATGGATCATGGTTTATCCAGTCCATTTGTGAAGTGTTCAACAAGCACATGCACAACATGGATGTGCTACGGATGATGACAAGAGTGAATAGCTTAGTGTCTACCTACCAGTCTAGAACAGGTGACTACTATTCTGATAGAAAGAAACAGGTTCCTAGTATTGTATCTATGCTCAGAAAagatctttttttctttcccgAGAATGTAACCCAGAATTAGGTGACCACATAGGACAGAGAAAATAGTGCTCTAAGGAATTCCAGAAGCACTCTGTTTCTAATTTGTATGCCAAAGAAagagaaacaagaaaaaacagaAGTATTGAAGCAGACCAGAATTTAGCCAGTGTTTTCGTAACATAGGATTCAATGGTTAGCAGCAAAGGTTTTGTCGAAAATTGACTTCTTTTTATACATCTTACTGTACTGGTAGTTGGGTTTGGCAATTTCCCTAAATTTGAATGTTTTGCTACCattctttttttcattagGAAGTACTGTATTATAATATAGGGTATTTTAAAACATATATCAATGTTCTATTGCTGGTGTTAATTTGCTGTAAATtgcatatttaaaaaaaaaaccctgttgTTTatcatgattaaaaaaataatgtttaagaCTAGAAAGGATACTATTTTACTAACCAGGAATGGAAGCTATGCTGCAATGGTTTTGAGGAAGACTGCAACATATGTATATAACCTAATtgttaattttaaaaacaattgaTGTTATAACTCATCATAGCAACATAATGTATTTCTACATAAATATTGATTTCTTACATTTGCAAacatgatatttttttgcacTTTATAGATAATGGCAAGTATGTGGATGTTAGAACTCACCGTAGTGATTGATTAAACTTAACAAGCAACACTAACTACTAGTTTGAGATGCAAAGACagacaaaaaacaaatgaTTGCATGAAAAAGTATGCAAACGTTTATGGATTAAGCTTAATCACTCTGTAGTTCTGTATCATTTTAAGATTTCTTGTAAAATCAAccttaatgtttttttatttatgaaaGGATCGTAGTTCTTGTTTTAGCTTGTTATTCATTATACAAAGAAGCTATAGGATAAAACTAATGAACTAATAAACAAAACTGTATGTGAggctaaaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q60431	Caspase-3 OS=Mesocricetus auratus OX=10036 GN=CASP3 PE=2 SV=1
F1NV61	Caspase-7 OS=Gallus gallus OX=9031 GN=CASP7 PE=3 SV=2
Q08DY9	Caspase-3 OS=Bos taurus OX=9913 GN=CASP3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001243 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00619 all species →	CARD	Caspase recruitment domain	Domain	Interproscan
PF00656 all species →	Peptidase_C14	Caspase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015917 all species →	Domain	Peptidase C14A, caspase catalytic domain	Interproscan
IPR001315 all species →	Domain	CARD domain	Interproscan
IPR029030 all species →	Homologous_superfamily	Caspase-like domain superfamily	Interproscan
IPR011029 all species →	Homologous_superfamily	Death-like domain superfamily	Interproscan
IPR033139 all species →	Active_site	Peptidase family C14A, cysteine active site	Interproscan
IPR011600 all species →	Domain	Peptidase C14, caspase domain	Interproscan
IPR001309 all species →	Domain	Peptidase C14, p20 domain	Interproscan
IPR002138 all species →	Domain	Peptidase C14, caspase non-catalytic subunit p10	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10454 all species →	CASPASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008234 all species →	Molecular Function	cysteine-type peptidase activity	Interproscan
GO:0042981 all species →	Biological Process	regulation of apoptotic process	Interproscan
GO:0004197 all species →	Molecular Function	cysteine-type endopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006915 all species →	Biological Process	apoptotic process	Interproscan
GO:0043525 all species →	Biological Process	positive regulation of neuron apoptotic process	Interproscan
GO:0097153 all species →	Molecular Function	obsolete cysteine-type endopeptidase activity involved in apoptotic process	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
K04397	CASP7; caspase 7	EC:3.4.22.60	Peptidases and inhibitors	ko01002	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_001633895.2 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

46TPM > 0

16Conditions

71.9Max TPM

37.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	34.43	37.14
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	24.63	31.61
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	31.48	39.35
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	59.71	71.87
whole 6 week old aboral regenerate · regenerate uncut	3	3	23.85	33.83
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	59.87	66.44
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	33.19	35.40
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	35.60	43.13
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	38.55	49.58
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	44.23	49.08
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	39.01	47.58
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	39.60	48.21
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	43.99	63.36
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	27.01	44.56
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	29.09	30.88
whole 6 week old aboral regenerate · regenerate 12hpa	3	2	31.23	48.02

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	37.14
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	33.12
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	33.02
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	31.61
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	22.23
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	20.06
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	39.35
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	27.83
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	27.28
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	71.87
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	60.19
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	47.06
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	33.83
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	22.39
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	15.33
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	66.44
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	59.30
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	53.87
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	35.40
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	33.82
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	30.34
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	43.13
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	33.73
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	29.96
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	49.58
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	33.35
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	32.73
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	49.08
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	42.13
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	41.49
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	47.58
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	35.74
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	33.72
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	48.21
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	35.91
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	34.69
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	63.36
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	36.31
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	32.29
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	44.56
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	36.49
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	30.88
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	30.20
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	26.18
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	48.02
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	45.68
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.