Detailed information of XP_001633835.2 in Nematostella vectensis

Genomic Location: NC_064043.1:9079347...9084337
NR annotation: XP_001633835.2, phytanoyl-CoA dioxygenase, peroxisomal [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
O14832Phytanoyl-CoA dioxygenase, peroxisomal OS=Homo sapiens OX=9606 GN=PHYH PE=1 SV=1
P57093Phytanoyl-CoA dioxygenase, peroxisomal OS=Rattus norvegicus OX=10116 GN=Phyh PE=1 SV=2
O35386Phytanoyl-CoA dioxygenase, peroxisomal OS=Mus musculus OX=10090 GN=Phyh PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006458 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF05721
all species →		PhyHPhytanoyl-CoA dioxygenase (PhyH)DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR047128
all species →		FamilyPhytanoyl-CoA dioxygenaseInterproscan
IPR008775
all species →		FamilyPhytanoyl-CoA dioxygenase-likeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR21308
all species →		PHYTANOYL-COA ALPHA-HYDROXYLASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0001561
all species →		Biological Processfatty acid alpha-oxidationInterproscan
GO:0048244
all species →		Molecular Functionphytanoyl-CoA dioxygenase activityInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K00477PHYH; phytanoyl-CoA hydroxylaseEC:1.14.11.18
Peroxisomeko04146deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_001633835.2 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
48TPM > 0
16Conditions
117.9Max TPM
79.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole 6 week old aboral regenerate · regenerate 96hpa 3 3 72.90 86.80
whole 6 week old aboral regenerate · regenerate 144hpa 3 3 71.24 84.10
whole 6 week old aboral regenerate · regenerate 0hpa 3 3 95.45 102.78
whole 6 week old aboral regenerate · regenerate 2hpa 3 3 79.62 85.24
whole 6 week old aboral regenerate · regenerate uncut 3 3 93.27 117.94
whole 6 week old aboral regenerate · regenerate 4hpa 3 3 63.52 79.28
whole 6 week old aboral regenerate · regenerate 120hpa 3 3 90.30 106.81
whole 6 week old aboral regenerate · regenerate 36hpa 3 3 71.89 77.40
whole 6 week old aboral regenerate · regenerate 24hpa 3 3 67.03 69.57
whole 6 week old aboral regenerate · regenerate 20hpa 3 3 72.69 83.61
whole 6 week old aboral regenerate · regenerate 16hpa 3 3 81.27 93.54
whole 6 week old aboral regenerate · regenerate 72hpa 3 3 84.09 111.44
whole 6 week old aboral regenerate · regenerate 60hpa 3 3 73.55 77.49
whole 6 week old aboral regenerate · regenerate 48hpa 3 3 79.79 101.54
whole 6 week old aboral regenerate · regenerate 8hpa 3 3 90.68 105.81
whole 6 week old aboral regenerate · regenerate 12hpa 3 3 84.86 91.39

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR6320863 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 86.80
SRR6320836 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 75.55
SRR6320837 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 56.34
SRR6320847 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 84.10
SRR6320838 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 69.98
SRR6320841 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 59.62
SRR6320840 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 102.78
SRR6320846 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 94.29
SRR6320839 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 89.27
SRR6320842 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 85.24
SRR6320848 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 83.90
SRR6320861 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 69.73
SRR6320845 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 117.94
SRR6320844 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 81.10
SRR6320843 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 80.75
SRR6320849 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 79.28
SRR6320872 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 61.44
SRR6320873 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 49.83
SRR6320850 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 106.81
SRR6320882 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 84.30
SRR6320883 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 79.79
SRR6320851 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 77.40
SRR6320855 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 74.15
SRR6320852 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 64.10
SRR6320853 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 69.57
SRR6320856 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 67.59
SRR6320854 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 63.94
SRR6320859 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 83.61
SRR6320860 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 73.54
SRR6320857 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 60.91
SRR6320881 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 93.54
SRR6320858 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 79.78
SRR6320880 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 70.50
SRR6320864 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 111.44
SRR6320862 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 80.20
SRR6320865 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 60.63
SRR6320867 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 77.49
SRR6320869 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 73.87
SRR6320866 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 69.29
SRR6320868 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 101.54
SRR6320870 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 70.62
SRR6320871 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 67.20
SRR6320876 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 105.81
SRR6320875 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 86.73
SRR6320874 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 79.49
SRR6320879 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 91.39
SRR6320878 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 85.62
SRR6320877 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 77.56

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.

Co-expression network

Genes whose expression across the transcriptome samples of Nematostella vectensis 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated2XP_032227903.10.723622470634346
Negatively correlated55XP_032237552.1-0.655170984086784

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 Nematostella vectensis, 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.

DatasetTissue / stageCellsCell typesThis geneMarker of
NVECT_2month2 month animal · Adult tissues/organs1,61423not in this dataset–
NVECT_bodywallbody wall with mesenteries · 6-8 weeks adults11,74213not in this dataset–
NVECT_embryoembryos · 8, 10 and 12 h after fertilisation (deposit labels 8h/10h/12h)9,71117not in this dataset–
NVECT_gastrulaBlastula-gastrula intermediate · Developmental stages49,16627not in this dataset–
NVECT_gastruloiddissociated and reaggregated embryos · 4-48 hpa36,5508not in this dataset–
NVECT_neoplasmneoplasm · Adult tissues/organs2,53216not in this dataset–
NVECT_nervousGastrula Cells · nervous system16,59027unmapped–
NVECT_notch48hembryos treated 24-48 hpf (DMSO vs LY411575) · 48 hpf19,0447not in this dataset–
NVECT_tentacletentacle · Adult tissues/organs7,97719not in this dataset–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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.

Peak calls overlapping this gene

AssaySamplePeaksRegion
ChIP-seqH3K27ac_gastrulae_24h3Distal Intergenic 2 · Promoter (<=1kb) 1
H3K27ac_planulae_4days3Distal Intergenic 2 · Promoter (<=1kb) 1
H3K4me2_gastrulae_24h8Distal Intergenic 5 · Promoter (<=1kb) 2 · 3' UTR 1
H3K4me2_planulae_4days3Distal Intergenic 2 · Promoter (<=1kb) 1
H3K4me2_polyps4Distal Intergenic 2 · Promoter (<=1kb) 1 · 3' UTR 1
H3K4me3_gastrulae_24h3Distal Intergenic 2 · Promoter (<=1kb) 1
H3K4me3_planulae_4days1Promoter (<=1kb) 1
H3K4me3_polyps3Promoter (<=1kb) 2 · Distal Intergenic 1
H3K27ac_Ncol3_negative1Promoter (<=1kb) 1
H3K27ac_Ncol3_positive1Promoter (<=1kb) 1
H3K27ac_Nep3_negative2Promoter (<=1kb) 2
H3K27ac_Nep3_positive2Promoter (<=1kb) 2
H3K36me3_planulae_4days6Promoter (1-2kb) 2 · Exon 2 · Intron 1 · Promoter (<=1kb) 1
H3K36me3_polyps2Promoter (1-2kb) 2
H3K4me1_gastrulae_24h8Distal Intergenic 4 · Promoter (<=1kb) 3 · Intron 1

5 further sample(s) also have peaks at this gene; open the assay page below to see them all.

Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.

DNA methylation (bisulphite samples)

SampleMethylation profile
Whole_adultsopen

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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