Gene detail

Detailed information of XP_001636071.2 in Nematostella vectensis

Genomic Location: NC_064047.1:7058369...7065729
NR annotation: XP_001636071.2, peptidyl-prolyl cis-trans isomerase-like 4 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_001636021.3

TTGTAGattgttttagatttttttttttaccattgcgcttggaaaaaacaaaatgccaCTTTTGACTTTCCCTTCTCCGGTAAGTCAAGACAATGTTCACATGTAGCGTGCACCGAACGTTCTTTATCAACGCGATCGTTTCGGAGGTTTCGGGGCAAATAACGCCAGTTTGCTATGTCATAGCCTAACTAAACTTACATAAAGTGACAACAAAACTTAAGCAGTGCTTGTAGGTTTGTATTTACACGTCACCCCATGTTTTGAGCGAATTTTGAAGCATGCTTTGTTGACAAGAGAAACGATGTCTGTTATCCTCGAAACCACTGTTGGGGATATTGTGGTGGATCTATTCACAGATGAACGCCCCCGAGCATGCCTGAATTTTCTGAAGTTGTGCAAGATCAAGTTCTACAACTATTGCCTTTTCCATTCAGTGCAGAGAAACTTCACTGCTCAAACAGGTGATCCACAAGGTACTGGAAAAGGTGGAGAGTCAGTTTTCagGGTATTATATGGTGACCAGGCAAAGTTTTTCAATGCTGAGGCCAAGCCACAACTAAAGCATAAAAACAAGGGCACAGTTTCCATGGTTAACAATGGTGACAATATGCATGGCTCACAATTCTTTATCACCCTTGCCGATGGCCTGGACTACCTGGATGGGGAGCACACAGTGTTTGGTGAGGTCTCTGAAGGTTTTGATGTCTTGGACAAGATTAATGAAGCTATTTGCACTGATGAATTTAGACCCTACCAGGATATAAGAATCACTCATACTGTCATTCTTGATGACCCGTTTGACGACCCTGAAGGGTTGCCCATTCCTGACCGTTCTCCCGAGCCAACCAAGGAGCAACTGGAGAGCGGACTAATAGGTGCAGACGAGGAGGTAGACGAAACTAAGGGCAAGACCATGGAGGAGATAGAAGACATGATTGAAGAGCGAGAGGAAAAAGCTGGTGCACAGCTTCTTGAAATGATTGGTGATATACCAGATGCCGATATCAAGCCTCCGGATAACGTCCTTTTTGTCTGCAAGTTGAACCCTGTTACCACTGACGAAGACTTGGAAATTATCTTCTCAAGATTTGGGACCATTCTTAGttGTGAAGTGATCCGAGACCAGAAAACAGGCGAATCTCTACAGTATGCATTCATTGAGTTTGAAAAAGACGAGGACTGTGAAAGAGCGTACTTTAAGATGGACAATGTCTTGATTGATGATCGACGAATTCATGTAGACTTCTCCCAATCTGTGTCAAAAATCAAATTGCAAATGAGAAAAGGAGCCCAGCCACCCTTTCCAGATAAAAAAGATGACAGGCCTAAATTTTCCATCAAGGATAAAGGCAAACGTGACAAATATGACCTGGTCTTTGACAACAATTCAAGTGACGATGACCAGCcgatgaagaagaaaaaatcctCAAAAAATGATGACAACAGAAAGTCAGAGAAagagaaatacaaagaaaaagatCAAAGGTCAAGGGAGAGAGATGAAGACGGACACAGAAAGAGAGATCGGGATAGAAGGGATGACAGGGACAGGAGAGGGGAGAGGAACAGAGATAAGgatAAAGATCATAGGGGTGACAGAAAAAGGTCTGATGACGATAGACAGGAGAAAAGCCGCAAGAGCAGACGGTCCCCTTCTCCGTACCGATCACGTGACCGAGATAGAAAACACAGAGATGACAGGAAACACAGATGATGGCATGTGATACCTGTGTGGAGCAATACTTGTCTTTTTATAAACACTGTTAAACAAGACTTCACCTACACGTAACCTTGGAAGATTGGCATTCCTGTGTTTGGCAGGCCACCTAGGACgattgggattcctgtgttttcCATAGCATCCCTAGGACGgctgggattcctgtgttttcTATAGGCTTccttgggattcctgtgtttgcCATATTTCTATGATGACacttgggattcctgtgtttggcATGTTTCGTATGACGATTAAATTTGATTGTGCTTGCCAGGTTCCCTAGTAAATAATGGCCACGATGGGTATCGTTCAATTTAAGTTCTCAAAGGACGAATGGAGAAGTGTAGCAGCCTGCTCATAAGGCCTAACATAACTGCCTGGATTACCTCATAGTTCTAATGTATTTAgttctgttgttttgtttccgATTGTTGTGTCTGTGGTGCATCAATCCAAGGAGGTGGAATCTTTTGATAGCCACTACATGACCcgatcattatttttttaaacaagggACTATTCTGTTGCCCGTGCGCATTTCATTGAGCGATTTGGCgatcaaaatggcggatgtGGAATGTTATGACAAAAACTCGCACTGTTTCTTGACTGTAGAGATATCTTTTTTGACCAGAAAATTCCCGCAGAAGGCAAAGATAATGTCTGTGAAGTAGTTTCGCTCGAATCAGCGATTGCCGGATACCGTTTTGCGTGCTAAATATAACCATAAAGATGCTAAACAGCTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8WUA2	Peptidyl-prolyl cis-trans isomerase-like 4 OS=Homo sapiens OX=9606 GN=PPIL4 PE=1 SV=1
Q9CXG3	Peptidyl-prolyl cis-trans isomerase-like 4 OS=Mus musculus OX=10090 GN=Ppil4 PE=1 SV=2
G5EEW6	Peptidyl-prolyl cis-trans isomerase sig-7 OS=Caenorhabditis elegans OX=6239 GN=sig-7 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004998 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF00160 all species →	Pro_isomerase	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR035542 all species →	Family	Cyclophilin-RNA interacting protein	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR035538 all species →	Domain	PPIL4-like, cyclophilin domain	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR002130 all species →	Domain	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain	Interproscan
IPR029000 all species →	Homologous_superfamily	Cyclophilin-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45843 all species →	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000413 all species →	Biological Process	protein peptidyl-prolyl isomerization	Interproscan
GO:0003755 all species →	Molecular Function	peptidyl-prolyl cis-trans isomerase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K12735	PPIL4; peptidyl-prolyl cis-trans isomerase-like 4	EC:5.2.1.8	Chaperones and folding catalysts	ko03110	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_001636071.2 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

37.9Max TPM

23.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	25.27	25.94
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	18.01	22.01
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	19.63	21.42
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	25.80	27.82
whole 6 week old aboral regenerate · regenerate uncut	3	3	18.68	19.75
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	24.36	24.72
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	21.11	23.82
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	29.59	32.90
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	27.59	30.36
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	31.76	37.87
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	25.49	29.09
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	22.93	27.05
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	24.48	26.33
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	20.16	31.93
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	21.61	23.69
whole 6 week old aboral regenerate · regenerate 12hpa	3	2	12.97	25.88

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	25.94
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	25.81
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	24.06
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	22.01
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	16.58
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	15.44
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	21.42
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	18.79
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	18.68
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	27.82
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	25.48
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	24.11
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	19.75
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	18.20
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	18.10
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	24.72
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	24.25
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	24.12
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	23.82
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	20.05
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	19.46
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	32.90
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	30.29
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	25.57
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	30.36
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	26.99
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	25.41
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	37.87
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	29.00
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	28.42
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	29.09
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	23.71
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	23.66
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	27.05
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	21.96
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	19.77
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	26.33
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	25.63
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	21.47
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	31.93
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	28.55
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	23.69
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	22.77
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	18.36
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	25.88
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	13.02
SRR6320878	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.