Detailed information of XP_048575989.1 in Nematostella vectensis

Genomic Location: NC_064045.1:9947537...9951709
NR annotation: XP_048575989.1, apolipoprotein D [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)
No Swiss-Prot hit above the reporting threshold for this gene.
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004109 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF08212
all species →		Lipocalin_2Lipocalin-like domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR012674
all species →		Homologous_superfamilyCalycinInterproscan
IPR022271
all species →		FamilyLipocalin, ApoD typeInterproscan
IPR000566
all species →		DomainLipocalin/cytosolic fatty-acid binding domainInterproscan
IPR047202
all species →		DomainLipocalin Blc-likeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10612
all species →		APOLIPOPROTEIN DInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000302
all species →		Biological Processresponse to reactive oxygen speciesInterproscan
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0006629
all species →		Biological Processlipid metabolic processInterproscan

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
No KEGG orthology assignment for XP_048575989.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_048575989.1 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
434.6Max TPM
249.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole 6 week old aboral regenerate · regenerate 96hpa 3 3 182.40 193.17
whole 6 week old aboral regenerate · regenerate 144hpa 3 3 147.20 167.85
whole 6 week old aboral regenerate · regenerate 0hpa 3 3 252.57 277.68
whole 6 week old aboral regenerate · regenerate 2hpa 3 3 268.25 276.94
whole 6 week old aboral regenerate · regenerate uncut 3 3 199.27 261.57
whole 6 week old aboral regenerate · regenerate 4hpa 3 3 254.25 283.54
whole 6 week old aboral regenerate · regenerate 120hpa 3 3 187.87 213.11
whole 6 week old aboral regenerate · regenerate 36hpa 3 3 222.30 250.05
whole 6 week old aboral regenerate · regenerate 24hpa 3 3 285.52 311.73
whole 6 week old aboral regenerate · regenerate 20hpa 3 3 373.40 434.56
whole 6 week old aboral regenerate · regenerate 16hpa 3 3 366.91 377.69
whole 6 week old aboral regenerate · regenerate 72hpa 3 3 209.61 258.17
whole 6 week old aboral regenerate · regenerate 60hpa 3 3 205.22 223.48
whole 6 week old aboral regenerate · regenerate 48hpa 3 3 211.22 275.99
whole 6 week old aboral regenerate · regenerate 8hpa 3 3 269.24 278.65
whole 6 week old aboral regenerate · regenerate 12hpa 3 3 349.94 356.21

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 193.17
SRR6320836 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 190.58
SRR6320837 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 163.46
SRR6320838 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 167.85
SRR6320847 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 161.38
SRR6320841 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 112.38
SRR6320846 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 277.68
SRR6320840 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 256.65
SRR6320839 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 223.38
SRR6320848 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 276.94
SRR6320861 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 272.57
SRR6320842 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 255.23
SRR6320843 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 261.57
SRR6320845 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 192.63
SRR6320844 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 143.62
SRR6320849 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 283.54
SRR6320873 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 262.51
SRR6320872 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 216.70
SRR6320850 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 213.11
SRR6320882 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 189.85
SRR6320883 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 160.66
SRR6320851 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 250.05
SRR6320855 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 219.57
SRR6320852 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 197.27
SRR6320854 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 311.73
SRR6320853 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 279.19
SRR6320856 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 265.65
SRR6320859 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 434.56
SRR6320860 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 371.89
SRR6320857 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 313.75
SRR6320880 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 377.69
SRR6320881 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 364.44
SRR6320858 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 358.61
SRR6320864 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 258.17
SRR6320862 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 209.92
SRR6320865 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 160.75
SRR6320869 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 223.48
SRR6320867 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 211.79
SRR6320866 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 180.39
SRR6320868 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 275.99
SRR6320870 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 181.90
SRR6320871 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 175.79
SRR6320876 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 278.65
SRR6320875 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 266.42
SRR6320874 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 262.65
SRR6320877 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 356.21
SRR6320879 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 356.04
SRR6320878 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 337.57

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 correlated17XP_048586979.10.910583104490731
Negatively correlated28XP_032220036.1-0.732259041822296

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/organs1,61423in viewerCluster 13 (3.773, 0.481%)
NVECT_bodywallbody wall with mesenteries · 6-8 weeks adults11,74213in viewerGastrodermis (3.172, 0.542%)
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–

Opening a dataset shows the UMAP with this gene coloured and the violin plot of its expression per cell type. 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-seqH3K36me3_polyps1Promoter (1-2kb) 1
H3K4me1_planulae_4days5Promoter (<=1kb) 2 · Promoter (1-2kb) 1 · Promoter (2-3kb) 1 · Exon 1
late_planula_4d4Promoter (<=1kb) 1 · Promoter (1-2kb) 1 · Intron 1 · Exon 1

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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