Gene detail

Detailed information of XP_032228367.2 in Nematostella vectensis

Genomic Location: NC_064046.1:14296124...14304265
NR annotation: XP_032228367.2, bifunctional polynucleotide phosphatase/kinase isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC5504195

ATGCTCGGCCGATATGGCAGACGAATCATAATATCGTTCTTTCCCGCCAAATACTTGAGTTTAACACGTTTACTAAGGATTAACAGATACTCTAGCTGCATACATAGGTTGGTAAACATGGAGTGTTTTCTGCATTCTTGTGAAAATACCCATCCACCCATTTCTTTACCCGACGGTGAGAAGGTCATTGTCGGTAGAAGCAGGGAGACCCAAGTCGCCGACAAGAAGTGTTCCAAAACCCAAGTGAAAATGACAGCAAACTATATGAAGAAAGAGGTTCTTATTGAACAGGTTGGCAACAACCCAAGCACTGTGAATAATAAAAACCTTCAGAAAGGAGAATCTGCTGTGCTAAGGCCTAGTGAAATGTTTGGTTTGTTGCATACAAACTATTTGCATTATATCACTTTCACAACATCCGGTCAACCATCCACACCTATAGCTGATGAATGGTCATCACAGGAGAAAAAGGACTCTCTCAGTTCTCCAAGCAAAAAGATAGACAGAAAAAGGGATGTTGATCAAGAAAACACAGAGACAAAAGGATTAGAGTTGAACAAAGTTAAACAGATTAAAGACAGTGAGAAATGCTTGGAAGCTATTGACTATGACTCTCTCAGTTCTCCAAGCAAAAAGATAGGAAATAAAAGGAAAATTGATCAAGAGAACACAGATACAAAACGATCTAAATTGAACATAGGTGAACTGATTCAAGGCAGTAAGAGGAGCTTGGAAGATATTGACTATGATGAAGTAAAGAAAGAGTTTGGTGAGGAAATGGTAGAAGAATTGAAGTCTAAACATAAGAAGATTGAAGATCTTGGCTGTTCTTCTGGTGTTGACAGTGCATTGAATCTAAACGGTGACAGTCAGCAGAATTTTGCCAATCCTAGTAATGCTTCGGAATGGAGTGAAATTCCAGGAGAGTTGCTGGTGTTCACATCCAAAGGTGTTGAGGGAAGAAAAAAGATTGCAGGTTTTGATCTCGATGGTACAATAATCACCACAAAATCTGGCAAAGTATTCCCCACCAACACTGCAGACTGGACGATTCTTTTTCCTCAAATCCCTGGAAAGCTGAAACAGTTATGGAGAGATGGTTATAAGATTGTCTTTTTCACCAATCAGAATGGTATAGCTAAGAAAAAAGTCAGTGTACCAGACTTCAAGGTGAAAATTCAGCGCATTTTGGATTTGCTTGGCGTACCAACACAGGTGCTAATATCTCCAGGGACTGGTCATTATCGAAAGCCTTGCACGGGAATGTGGAAATATCTTCTTGAAAAAGCAAACCAGTCAGTTCCTGTCAACAAAGAAGAATGCATGTATATTGGAGATGCTGCTGGCCGTCCTGTAAACTGGGAGCCAAAGAAAAAGAAAGACTTTTCATGTAGCGATCGAACTTTCGCTGCGAAAATCGACATAAAATTCTACACACCCGAAGAGTTCTTTTTGGGCAAAAAACCTGCTCCCTTCAACTGGCCCGTATTTAATCCGCGAAAACTACTTGATGGCAATAGACCTCTGTTTACACCGACTTCGTCAAATCTAACATCGAATACCCCAGAGCTGATTGTGATGGTTGGGTCCCCAGGATCCGGTAAGACGACTTTTGCAAAGGAATACCTCGTTCCCAAAGGTTACACACGCATTAACAGGGACACTTTGGGCACATGGCAGAAGTGCGTGTCTGCGTGTCGCGCAGCCCTGTCACAGGGAAAACACGTGGTGGTCGACAACACTAACCCTGACCAGGAGTCCAGAAAAAGGTATATCGAGTGCGCAAAGCACGCTAAAGTTCCTGTTCGTTGCTTTGTTATGGACATTTCCCTGGAGCACGCCAAACACAACAATGCCGTGCGAGAGATGACAAACACCGACAGTTCGTACAAACATGTCGGGTTCATGGCGTTCAACAGTTACAAATCTAGCTACAAAGAGCCCTCGGTCAGTGAAGGATTCGACGAGATCTTGAAGATCCACTTCAAAGCTGTGTTCAAAAACCAAGAGACTAGGGATCTGTATATGCAGTCCTTACATACCTAG

Transcript

rna-XM_032372476.2

TGGTGTAAATTAGAAACCATACTTCAGCAGGAATGCTCGGCCGATATGGCAGACGAATCATAATATCGTTCTTTCCCGCCAAATACTTGAGTTTAACACGTTTACTAAGGATTAACAGATACTCTAGCTGCATACATAGGTTGGTAAACATGGAGTGTTTTCTGCATTCTTGTGAAAATACCCATCCACCCATTTCTTTACCCGACGGTGAGAAGGTCATTGTCGGTAGAAGCAGGGAGACCCAAGTCGCCGACAAGAAGTGTTCCAAAACCCAAGtgaaAATGACAGCAAACTATATGAAGAAAGAGGTTCTTATTGAACAGGTTGGCAACAACCCAAGCACTGTGAATAATAAAAACCTTCAGAAAGGAGAATCTGCTGTGCTAAGGCCTAGTGAAATGTTTGGTTTGTTGCATACAAACTATTTGCATTATATCACTTTCACAACATCCGGTCAACCATCCACACCTATAGCTGATGAATGGTCATCACAGGAGAAAAAGGACTCTCTCAGTTCTCCAAGCAAAAAGATAGACAGAAAAAGGGATGTTGATCAAGAAAACACAGAGACAAAAGGATTAGAGTTGAACAAAGTTAAACAGATTAAAGACAGTGAGAAATGCTTGGAAGCTATTGACTATGACTCTCTCAGTTCTCCAAGCAAAAAGATAGGAAATAAAAGGAAAATTGATCAAGAGAACACAGATACAAAACGATCTAAATTGAACATAGGTGAACTGATTCAAGGCAGTAAGAGGAGCTTGGAAGATATTGACTATGATGAAGTAAAGAAAGAGTTTGGTGAGGAAATGGTAGAAGAATTGAAGTCTAAACATAAGAAGATTGAAGATCTTGGCTGTTCTTCTGGTGTTGACAGTGCATTGAATCTAAACGGTGACAGTCAGCAGAATTTTGCCAATCCTAGTAATGCTTCGGAATGGAGTGAAATTCCAGGAGAGTTGCTGGTGTTCACATCCAAAGGTGTTGAGGGAAGAAAAAAGATTGCAGGTTTTGATCTCGATGGTACAATAATCACCACAAAATCTGGCAAAGTATTCCCCACCAACACTGCAGACTGGACgaTTCTTTTTCCTCAAATCCCTGGAAAGCTGAAACAGTTATGGAGAGATGGTTATAAgATTGTCTTTTTCACCAATCAGAATGGTATAGCTAAGAAAAAAGTCAGTGTACCAGACTTCAAGGTGAAAATTCAGCGCATTTTGGATTTGCTTGGCGTACCAACACAGGTGCTAATATCTCCAGGGACTGGTCATTATCGAAAGCCTTGCACGGGAATGTGGAAATATCTTCTTGAAAAAGCAAACCAGTCAGTTCCTGTCAACAAAGAAGAATGCATGTATATTGGAGATGCTGCTGGCCGTCCTGTAAACTGGGAgccaaagaaaaagaaagactTTTCATGTAGCGATCGAACTTTCGCTGCGAAAATCGACATAAAATTCTACACACCCGAAGAGTTCTTTTTGGGCAAAAAACCTGCTCCCTTCAACTGGCCCGTATTTAATCCGcGAAAACTACTTGATGGCAATAGACCTCTGTTTACACCGACTTCGTCAAATCTAACATCGAATACCCCAGAGctgATTGTGATGGTTGGGTCCCCAGGATccGGTAAGACGACTTTTGCAAAGGAATACCTCGTTCCCAAAGGTTACACACGCATTAACAGGGACACTTTGGGCACATGGCAGAAGTGCGTGTCTGCGTGTCGCGCAGCCCTGTCACAGGGAAAACACGTGGTGGTCGACAACACTAACCCTGACCAGGAGTCCAGAAAAAGGTATATCGAGTGCGCAAAGCACGCTAAAGTTCCTGTTCGTTGCTTTGTTATGGACATTTCCCTGGAGCACGCCAAACACAACAATGCCGTGCGAGAGATGACAAACACCGACAGTTCGTACAAACATGTCGGGTTCATGGCGTTCAACAGTTACAAATCTAGCTACAAAGAGCCCTCGGTCAGTGAAGGATTCGACGAGATCTTGAAGATCCACTTCAAAGCTGTGTTCAAAAACCAAGAGACTAGGGATCTGTATATGCAGTCCTTACATACCTAGGGAGATCTAAATGATCAGATGATCGGAATCTTGTTGTATTTGAACGCGAAAAAGTGGGTTTTGGCAGGCCGTCTCGAAGCTTTCTGGAACGTAGGCTAAGTTCacacgtcgtattatccatgagccgtattcaatgcaaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9JLV6	Bifunctional polynucleotide phosphatase/kinase OS=Mus musculus OX=10090 GN=Pnkp PE=1 SV=2
Q96T60	Bifunctional polynucleotide phosphatase/kinase OS=Homo sapiens OX=9606 GN=PNKP PE=1 SV=1
Q19683	Uncharacterized protein F21D5.5 OS=Caenorhabditis elegans OX=6239 GN=F21D5.5 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002702 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13671 all species →	AAA_33	AAA domain	Domain	Interproscan
PF08645 all species →	PNK3P	Polynucleotide kinase 3 phosphatase	Family	Interproscan
PF17913 all species →	FHA_2	FHA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006549 all species →	Domain	HAD-superfamily hydrolase,subfamily IIIA	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR036412 all species →	Homologous_superfamily	HAD-like superfamily	Interproscan
IPR006551 all species →	Domain	Polynucleotide 3'-phosphatase	Interproscan
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR006550 all species →	Family	Bifunctional polynucleotide phosphatase/kinase PNKP	Interproscan
IPR013954 all species →	Family	Polynucleotide kinase 3 phosphatase	Interproscan
IPR041388 all species →	Domain	PNK, FHA domain	Interproscan
IPR023214 all species →	Homologous_superfamily	HAD superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12083 all species →	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0046403 all species →	Molecular Function	polynucleotide 3'-phosphatase activity	Interproscan
GO:0046404 all species →	Molecular Function	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	Interproscan
GO:0003690 all species →	Molecular Function	double-stranded DNA binding	Interproscan
GO:0046939 all species →	Biological Process	obsolete nucleotide phosphorylation	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
K08073	PNKP; bifunctional polynucleotide phosphatase/kinase	EC:3.1.3.32 EC:2.7.1.78	DNA repair and recombination proteins	ko03400	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_032228367.2 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

22.7Max TPM

14.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	15.86	16.56
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	14.12	19.56
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	15.77	16.80
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	17.20	19.79
whole 6 week old aboral regenerate · regenerate uncut	3	3	12.65	14.30
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	14.32	16.86
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	15.87	19.02
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	14.63	16.84
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	13.97	16.46
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	13.16	14.31
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	12.89	14.08
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	18.56	22.70
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	15.21	17.15
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	12.08	19.04
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	17.19	18.96
whole 6 week old aboral regenerate · regenerate 12hpa	3	3	12.72	15.99

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	16.56
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	16.04
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	14.98
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	19.56
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	12.22
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	10.58
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	16.80
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	15.32
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	15.18
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	19.79
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	16.54
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	15.29
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	14.30
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	13.74
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	9.92
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	16.86
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	14.02
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	12.09
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	19.02
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	15.49
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	13.11
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	16.84
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	14.03
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	13.03
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	16.46
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	14.47
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	10.97
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	14.31
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	12.99
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	12.17
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	14.08
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	13.65
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	10.93
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	22.70
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	17.36
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	15.61
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	17.15
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	15.45
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	13.02
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	19.04
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	17.20
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	18.96
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	17.27
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	15.35
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	15.99
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	11.54
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	10.62

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.