Gene detail

Detailed information of XP_066919468.1 in Clytia hemisphaerica

Genomic Location: NW_027103829.1:446360...451924
NR annotation: XP_047135003.1, phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha-like isoform X2 [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

XP_066919468.1

ATGACAACTAGTCCGGTGGATTTGATATCCTTCGACGAATTTAAACCTAAAGTACCACCAAAAAGCAAACAACGTACTTTTTCTCCACCGCCGTTTCCACCAGCCGTAAAGAGGGAGCCAGACATCCGGCGTGTCATCTTATCAGAATTAGAATACTATCGCCCTTCATCTGCACAATCGAACAATAATTACGCATCCAATCTCGCCTTTCAAGATTTCACTGAGGGTGCAAACAACACAAATCTCAATGGCGGTGTCAATAACAATGCGCTCGAAAACGACAGTAGATGTGTATCAAACCCAGACACTTTAATAAACAATGAAACAGAATCAACTCAAAACTTTACCGAGAACAATAACACTGATGGACCACCCCTTCCCCCAAAGAAATATGGGCGTTCAAGGGCGAATGCACTTGAAAGACAAGTTTCTCTGACAAGAGGTGAAAAGCCAAAAAGAGACGACGAACTTAGTCCAGATGTGTTGAGTAAATCTATGCCGGATACTTTATACTTGTTCGACCCCTTCCTAAGTGAAAGTTTTATCGACGAGCCGACTATCGTCCGGGGAAGCCAAATATCGGACGGGGGTCGAACCGTACGTAGCAAAACAATGGTCGATGATAAGAACGTTGTTCCGACTTTCGATTTGCTTCAGTTCGATATTGATATTGATGAAACCAAGGATGAGACTTCGGTTGAAAGTGAAGTTAAATTGAAATCACCCACCTATCGTTTGAGCGAGCGACGGAAAGTTAAAACTCTCTCGCCTGAAGATTTACAACGATTCGAACGCTCGTCATCAGAGAAGAATCAATCGAATATTAACAAAGAAACGAAAACGAAAACGCTACCTGCGCGACCGCCGAGACCGAAAAACCGCTTTTCATGCCCGCCAAACGTGATTGCGGGGATCGGGGAGAACAGTCACAAAAATGGTTCTGATCAGAAAGACAGCTCGACAGCAGAACAATCCAACAACAAAAACGACATTTATTTCAAAACGGCGTTATTCCAACGTACAGAAGAACGTAACGAGGAAGCAGTAGCTTTCAGTAACGCCATCGCCAAATTACGTAAATTCTACAAACACGAAGATAAATCAACGAACATTGGTTGCATCGCACCTTCAAAAATCGCAAACAAAGCTTTATTGGACTCAACAGTCGAATTCACCATTTATTTCGACCCTGATCCTAAACCCAAAACAATGACGTGTAAACTCTCTTTAACCCCAACAGAAGTTATCCATAAATTCTTCACGGAGTGTTATAACGGTGGCAAAAGTTTTGAGTTAGATATTATCGCTGAACAATACGTTTTGAAATTCGTAGGTGCAACTACTTGTTTATCTGAACAATGCCCGTTATGTGATTACGTCACCATACAAGAATCTATCAAATATGGTTACCGTATTGAACTTGTGTTAGTCCGTACCGGGTTCGTCAACCTTGATTTTAAACGAGACGCGGAAGATGATACGGAAGATTGTCATAGCACGTATTTTAAGTATTATTTCGAAGAGAAGCAAACAAGCAGCTTGTCTATATCAGAGCAAGGGTTATCAGTACTTCTAGAGACTTACGATAGCGAAGCAGCCAGGCTTATGCAGGACGTCTCTGAAAGTCACAAAGTGACTTACCATCCTCAACGTATCATCCAAGTCGTGAAAGCAATCACGAAATCTCTTGCACAAGTCGAACTGTTAACTGTTCAAGAAGGTGTAAACATGTTGTTATCGTTAAAGAAATTCACTGCCCATTCCAAAAGTTTTTCCGCCCAAAGGACAGACGGGCGTAAAGAGGTGGTAGAATTTATGAACCCTATTCATTTTGATCATCAAAAGTTCCATTCTGCACTTCAAACTCTAACCCAGGGCGTTCATTCACTTATACAACTTTACTGCAAATTTTTCAACACTGATTTTAAGATACAGGACTTTGGCTCAAATAATATCAAAATCGATCAAAACGATATATTTGAGCGAATCGATCCACGAACGATTGACGATCGATTCACTGTTCGAATCGGATCCATACACCGTATACCCCACTCTTGGAAAACAACCTATACCGAGTTTGAAATTGAGGCTTCTCTTTACTACGGTGGAAATTTAACTGCAACACCTAAAAGAACAGCCAAAGCGAGAGTTTGCGTCGGCTTTTTTGAACATATACGCTTCCATGAGCTGTTAGAATTCGATGTATCGGTTCGTAACATCCCACGAGAATCAAAAGTAACTTTTAAGTTAATCGGACTTTCGCCGCCCAAGAAGGGTGGAGATGGGCGTACCACCCTCGGATGGGTCTCGTCAAATGTTTATGATCACCAAGGATTTCTCATGTCCGGGAGTCGACTTTTCGGACTGCTCTCCGAAGTACATTTCAATCCAGTCGCCACATGTGCTACTGGATACATCCAAAAACCCGAAACGGTCATTTTGAAAACCGATTTTCAAGTTTATCACACTGAAGTCTTGTTCCCACAACCTGTCCTCATAACGCAAACGTCAATTAACGGGAATCCGTCAACGTTATCCGAAGCTGAAATGACATACGTTACCAAGATCTTACGTAAAGATTCTCGTGTATTGACGCAAGAAGAACGTTACGTCATTTGGAAATCACGTTACGGTTTATGTCACCTACCTTACGCTTTGAAACACGTCTTGGCGTCTTGTCCTTCTTGGGACTCCATCAACGTTACAGAAGTTCATACGATCCTTAGTATGTGGGAAGCCTTGTCACCAAATGAAGCTATCGAGTTTCTACAAGCTGATTTCCCCGACAAAACAGTTCGTGAGACAGCCGTTTTGTGGTTATCGAGTATCACAGATTACGATCTAGTCGACTATTTGCCTGAGCTGGTCCAAGCCATCAAGTATGAAGCGTATCATGATTCGGCACTCGCTCAGTTCGTCATCAAGCGTTCCTTATCAAGTCCGAGTGTCGCTCATTTCTTGTTTTGGCATCTGAAGTATTACACAGGGGATCTTCAGTTCAGCCAACGTTTTCAAATTGTGTTGAGTGGTTTATTGAGTGCTTGTGGTCGGCGCATGCGTGCTCAGCTGCAACAACAAGATAACCTGATGGTAGAGCTCGCTCAAGTCTCTCTGAAAGTCAAGGCGTGTAAGGAGCCTACACGTCAATTATTACTTGTCAAGGAGCTACACAAAGTTAATGAAAGCAACGTCGAATTCCCCGTTCGCTCACCCATCGACCCATCACTCAAACTTGGTGAAATCTTACCTGAAAGCTCGTCGTATTTCTCCAGTCATACCGTCCCTTTGAAAATTTGTATGCGAAACGTAGACCGCCGTGGACGTGATATAAACTTCATTTTCAAGATCGGTGACGATTTACGAAAGGATTTAGTGACTCTTCTTATGTTTCGTGTTATGAATAAACTCTGGTTAAACGAAGGTCTTGACCTCAAGATGATGTTGTATAACGTTCTACCGACCGGCCCTCTGAGCGGCCTCATTGAGATTATACCGAACGCTGCCACGTTCCGTGAAATACACATACAGCATGGCTTAACCGGTTCATTCAAAGACGACTCGCTGATTTTATGGCTTCAACGTTTCAACACTACCGAACAAGATTATCACCGCGCGATCGACAATTTCACGTATTCGGCCGCCGGATATTGCGTAGCGACCTATCTACTCGGTATTGGAGATCGACACAACGATAACATCATGTTAACAAAGAACGGACATCTGTTCCATATCGACTTCTCGAAATTCATGGGAGATGTACAAAAGTTCGGTGCCATTAGTCGTGATCGGGTACCGTTCGTTCTAACACCGGATATGGCTTACGTCATCAACAACGGCATCACACCAACACAAAACTTTCAAAAGTTCATCGAGTACTGTTGTCAAGCTTTCAACATTATCCGTCGCAACAAACACGTCATTCTGAATTTACTCGGTCTGATGGTGTATTCGGGTATACCGTATTTATCTGAGAAAGAAGACCTCTTGTTCGTCCGAAAAAATCTCCAACTCGATCTAACAGACGAAGAAGCCACCATGTATTTTACCCGACTAATCGAGTCCAGTTTATCATCTCGTTCAACCCAACTGAACTTTTTCATACACAACATCGCACACATGAAAAACACCAGCGAGGCAACCCTTGGAAGCGCCAAATCAAGCCCCTTATTTTCGTTTTCTAACAAGACGCATACTCAAGCCAAAGACGGCGTTATCAATTCAGCTCGTATTGTTGATTTTCAGAAACGATACTTACCTGAGAAGCATTATGTTTTTGTTATCAACGTCACGCGGAAAGGCGTCAAAGAGCCAAAATTCGTTTTTCGTCGTTTCGAAGATTTTCAGGAACTCCATGCAAAGTTGAGTTACAAGTTCAATCCTTTCACCGGCACTATTATGCCGGAATTACCGGCCCGTATTGTTCTCGGACGGAGCCAGATCCGCGAGGTTGCGCACCGAAGGCGCTACGAATTAGACAACTATCTTGTGGCGTTATCGAAACTTGAAGATGTTTGGAGTTCTGATATTTTGTATACGTTCTTACATAGTTACATAAAGGATACGGAAGAGGCACGCCGTTTTGCAGAATACGTAGAATTATTAGCGGACGGACCCAAAACACGGATCGGTGGCAAAATCAAAGTTTCAATTGGGTATAAAAATAAAGCCTTACATGTTCTTGTGATGCATTGTAGCGGCTTAGTTCCTGATCGCGTCCAAGGGCTTGCTGACTCATTTGTTAAAGTTCGCATCATCCCTGACCCTTTACACCACTACAAACGAAAGACCCGAATCTGTCGAAAAACTTTACACCCTACTTTTAACGAGACTTTGATTTTTGAGGCGAGTTGGGAAATGTTACGGAAACGTGTTTTGCAAATTACTGTATGGGACAGTAATCATTTGATGGATAAAGAGTTCTTAGGTGGAGTGAATTGTTATTTGTCAACCTTCGATGTGAAGAAAACACAGAATGCTTGGTTCCCTCTAACTGATATTCAAATTTCTTAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5RAY1	Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha OS=Pongo abelii OX=9601 GN=PIK3C2A PE=2 SV=1
O00443	Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha OS=Homo sapiens OX=9606 GN=PIK3C2A PE=1 SV=2
O00750	Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta OS=Homo sapiens OX=9606 GN=PIK3C2B PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001304 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00792 all species →	PI3K_C2	Phosphoinositide 3-kinase C2	Domain	Interproscan
PF00454 all species →	PI3_PI4_kinase	Phosphatidylinositol 3- and 4-kinase	Family	Interproscan
PF00787 all species →	PX	PX domain	Domain	Interproscan
PF00613 all species →	PI3Ka	Phosphoinositide 3-kinase family, accessory domain (PIK domain)	Repeat	Interproscan
PF00794 all species →	PI3K_rbd	PI3-kinase family, ras-binding domain	Domain	Interproscan
PF00168 all species →	C2	C2 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001683 all species →	Domain	Phox homology	Interproscan
IPR035892 all species →	Homologous_superfamily	C2 domain superfamily	Interproscan
IPR000403 all species →	Domain	Phosphatidylinositol 3-/4-kinase, catalytic domain	Interproscan
IPR002420 all species →	Domain	C2 phosphatidylinositol 3-kinase-type domain	Interproscan
IPR015433 all species →	Family	Phosphatidylinositol kinase	Interproscan
IPR036871 all species →	Homologous_superfamily	PX domain superfamily	Interproscan
IPR000008 all species →	Domain	C2 domain	Interproscan
IPR001263 all species →	Domain	Phosphoinositide 3-kinase, accessory (PIK) domain	Interproscan
IPR018936 all species →	Conserved_site	Phosphatidylinositol 3/4-kinase, conserved site	Interproscan
IPR036940 all species →	Homologous_superfamily	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR000341 all species →	Domain	Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan
IPR011009 all species →	Homologous_superfamily	Protein kinase-like domain superfamily	Interproscan
IPR042236 all species →	Homologous_superfamily	Phosphoinositide 3-kinase, accessory (PIK) domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10048 all species →	PHOSPHATIDYLINOSITOL KINASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005942 all species →	Cellular Component	phosphatidylinositol 3-kinase complex	Interproscan
GO:0014065 all species →	Biological Process	obsolete phosphatidylinositol 3-kinase signaling	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016303 all species →	Molecular Function	1-phosphatidylinositol-3-kinase activity	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0035005 all species →	Molecular Function	1-phosphatidylinositol-4-phosphate 3-kinase activity	Interproscan
GO:0036092 all species →	Biological Process	phosphatidylinositol-3-phosphate biosynthetic process	Interproscan
GO:0046854 all species →	Biological Process	phosphatidylinositol phosphate biosynthetic process	Interproscan
GO:0048015 all species →	Biological Process	phosphatidylinositol-mediated signaling	Interproscan
GO:0052742 all species →	Molecular Function	phosphatidylinositol kinase activity	Interproscan
GO:0016301 all species →	Molecular Function	kinase 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
K00923	PIK3C2; phosphatidylinositol-4-phosphate 3-kinase	EC:2.7.1.154	Salmonella infection	ko05132	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_066919468.1 across 40 RNA-seq samples of Clytia hemisphaerica. 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.

40Samples

40TPM > 0

16Conditions

15.7Max TPM

6.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Mature medusa	5	5	5.99	9.74
medusa · Experiment Condition A1	4	4	3.00	3.17
medusa · Experiment Condition A2	4	4	4.47	4.97
medusa · Experiment Condition A3	4	4	6.73	7.62
Early gastrula	2	2	14.92	15.71
Planula 24hpf	2	2	11.97	12.36
Planula 48hpf	2	2	6.03	7.79
Planula 72hpf	2	2	5.09	6.31
Primary polyp	2	2	4.21	4.32
Gastrozooid	2	2	5.18	5.66
Gonozooid	2	2	6.35	6.75
Stolon	2	2	4.74	5.48
Baby medusa	2	2	5.93	6.10
medusa · Experiment Condition B1	2	2	6.34	6.77
medusa · Experiment Condition B2	2	2	3.89	3.99
Mixed	1	1	5.56	5.56

Per sample · hover a bar for the full sample record

Show the sample table (40 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
ERR2816251	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	9.74
ERR2816250	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	8.54
ERR2862245	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	5.00
ERR2816249	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	4.19
ERR2816248	Mature medusa	not recorded	Mature medusa	not recorded	ERP110164	2.49
ERR3299476	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	3.17
ERR3299475	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	3.15
ERR3299477	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	2.99
ERR3299478	medusa · Experiment Condition A1	not recorded	medusa	Experiment Condition A1	ERP115020	2.69
ERR3299479	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	4.97
ERR3299480	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	4.52
ERR3299481	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	4.47
ERR3299482	medusa · Experiment Condition A2	not recorded	medusa	Experiment Condition A2	ERP115020	3.93
ERR3299483	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	7.62
ERR3299484	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	7.21
ERR3299486	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	6.29
ERR3299485	medusa · Experiment Condition A3	not recorded	medusa	Experiment Condition A3	ERP115020	5.81
ERR2816230	Early gastrula	not recorded	Early gastrula	not recorded	ERP110164	15.71
ERR2816231	Early gastrula	not recorded	Early gastrula	not recorded	ERP110164	14.13
ERR2816233	Planula 24hpf	not recorded	Planula 24hpf	not recorded	ERP110164	12.36
ERR2816232	Planula 24hpf	not recorded	Planula 24hpf	not recorded	ERP110164	11.59
ERR2816235	Planula 48hpf	not recorded	Planula 48hpf	not recorded	ERP110164	7.79
ERR2816234	Planula 48hpf	not recorded	Planula 48hpf	not recorded	ERP110164	4.27
ERR2816236	Planula 72hpf	not recorded	Planula 72hpf	not recorded	ERP110164	6.31
ERR2816237	Planula 72hpf	not recorded	Planula 72hpf	not recorded	ERP110164	3.88
ERR2816239	Primary polyp	not recorded	Primary polyp	not recorded	ERP110164	4.32
ERR2816238	Primary polyp	not recorded	Primary polyp	not recorded	ERP110164	4.11
ERR2816240	Gastrozooid	not recorded	Gastrozooid	not recorded	ERP110164	5.66
ERR2816241	Gastrozooid	not recorded	Gastrozooid	not recorded	ERP110164	4.71
ERR2816242	Gonozooid	not recorded	Gonozooid	not recorded	ERP110164	6.75
ERR2816243	Gonozooid	not recorded	Gonozooid	not recorded	ERP110164	5.95
ERR2816245	Stolon	not recorded	Stolon	not recorded	ERP110164	5.48
ERR2816244	Stolon	not recorded	Stolon	not recorded	ERP110164	3.99
ERR2816246	Baby medusa	not recorded	Baby medusa	not recorded	ERP110164	6.10
ERR2816247	Baby medusa	not recorded	Baby medusa	not recorded	ERP110164	5.77
ERR3299472	medusa · Experiment Condition B1	not recorded	medusa	Experiment Condition B1	ERP115020	6.77
ERR3299471	medusa · Experiment Condition B1	not recorded	medusa	Experiment Condition B1	ERP115020	5.91
ERR3299473	medusa · Experiment Condition B2	not recorded	medusa	Experiment Condition B2	ERP115020	3.99
ERR3299474	medusa · Experiment Condition B2	not recorded	medusa	Experiment Condition B2	ERP115020	3.79
ERR2862244	Mixed	not recorded	Mixed	not recorded	ERP110164	5.56

Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM, StringTie quantification over 40 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.

Co-expression network

Genes whose expression across the transcriptome samples of Clytia hemisphaerica tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	28	XP_066932622.1	0.949338432725823
Negatively correlated	5	XP_066919317.1	-0.79452289903532

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Clytia hemisphaerica, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →