Detailed information of XP_001636882.2 in Nematostella vectensis

Genomic Location: NC_064035.1:8856562...8860591
NR annotation: XP_001636882.2, 60S ribosomal protein L23 [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
Q3T057Large ribosomal subunit protein uL14 OS=Bos taurus OX=9913 GN=RPL23 PE=2 SV=2
P62829Large ribosomal subunit protein uL14 OS=Homo sapiens OX=9606 GN=RPL23 PE=1 SV=1
Q90YU5Large ribosomal subunit protein uL14 OS=Ictalurus punctatus OX=7998 GN=rpl23 PE=2 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007610 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00238
all species →		Ribosomal_L14Ribosomal protein L14p/L23eDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036853
all species →		Homologous_superfamilyLarge ribosomal subunit protein uL14 superfamilyInterproscan
IPR000218
all species →		FamilyLarge ribosomal subunit protein uL14Interproscan
IPR019972
all species →		Conserved_siteLarge ribosomal subunit protein uL14, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11761
all species →		50S/60S RIBOSOMAL PROTEIN L14/L23Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003735
all species →		Molecular Functionstructural constituent of ribosomeInterproscan
GO:0005840
all species →		Cellular ComponentribosomeInterproscan
GO:0006412
all species →		Biological ProcesstranslationInterproscan
GO:0022625
all species →		Cellular Componentcytosolic large ribosomal subunitInterproscan
GO:0070180
all species →		Molecular Functionlarge ribosomal subunit rRNA bindingInterproscan

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
K02894RP-L23e, RPL23; large subunit ribosomal protein L23e-Ribosomeko03011deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_001636882.2 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
6,676.9Max TPM
5,647.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole 6 week old aboral regenerate · regenerate 96hpa 3 3 4,889.57 5,091.04
whole 6 week old aboral regenerate · regenerate 144hpa 3 3 4,880.98 5,456.12
whole 6 week old aboral regenerate · regenerate 0hpa 3 3 6,210.90 6,444.72
whole 6 week old aboral regenerate · regenerate 2hpa 3 3 6,006.86 6,276.32
whole 6 week old aboral regenerate · regenerate uncut 3 3 5,723.13 6,450.57
whole 6 week old aboral regenerate · regenerate 4hpa 3 3 6,244.78 6,676.94
whole 6 week old aboral regenerate · regenerate 120hpa 3 3 5,389.60 6,187.52
whole 6 week old aboral regenerate · regenerate 36hpa 3 3 5,477.05 5,671.24
whole 6 week old aboral regenerate · regenerate 24hpa 3 3 5,754.83 6,156.96
whole 6 week old aboral regenerate · regenerate 20hpa 3 3 5,666.50 6,286.75
whole 6 week old aboral regenerate · regenerate 16hpa 3 3 5,751.22 5,868.53
whole 6 week old aboral regenerate · regenerate 72hpa 3 3 5,036.70 5,232.67
whole 6 week old aboral regenerate · regenerate 60hpa 3 3 5,591.47 6,380.62
whole 6 week old aboral regenerate · regenerate 48hpa 3 3 5,397.59 5,958.13
whole 6 week old aboral regenerate · regenerate 8hpa 3 3 6,049.90 6,288.93
whole 6 week old aboral regenerate · regenerate 12hpa 3 3 6,292.30 6,664.69

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 5,091.04
SRR6320836 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 5,022.63
SRR6320837 whole 6 week old aboral regenerate · regenerate 96hpa whole 6 week old aboral regenerate six weeks regenerate 96hpa SRP125570 4,555.05
SRR6320838 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 5,456.12
SRR6320847 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 5,233.79
SRR6320841 whole 6 week old aboral regenerate · regenerate 144hpa whole 6 week old aboral regenerate six weeks regenerate 144hpa SRP125570 3,953.02
SRR6320840 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 6,444.72
SRR6320839 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 6,119.95
SRR6320846 whole 6 week old aboral regenerate · regenerate 0hpa whole 6 week old aboral regenerate six weeks regenerate 0hpa SRP125570 6,068.03
SRR6320848 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 6,276.32
SRR6320861 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 5,875.71
SRR6320842 whole 6 week old aboral regenerate · regenerate 2hpa whole 6 week old aboral regenerate six weeks regenerate 2hpa SRP125570 5,868.56
SRR6320845 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 6,450.57
SRR6320843 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 5,709.61
SRR6320844 whole 6 week old aboral regenerate · regenerate uncut whole 6 week old aboral regenerate six weeks regenerate uncut SRP125570 5,009.21
SRR6320873 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 6,676.94
SRR6320849 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 6,198.62
SRR6320872 whole 6 week old aboral regenerate · regenerate 4hpa whole 6 week old aboral regenerate six weeks regenerate 4hpa SRP125570 5,858.77
SRR6320850 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 6,187.52
SRR6320882 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 5,137.84
SRR6320883 whole 6 week old aboral regenerate · regenerate 120hpa whole 6 week old aboral regenerate six weeks regenerate 120hpa SRP125570 4,843.44
SRR6320851 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 5,671.24
SRR6320855 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 5,551.82
SRR6320852 whole 6 week old aboral regenerate · regenerate 36hpa whole 6 week old aboral regenerate six weeks regenerate 36hpa SRP125570 5,208.07
SRR6320856 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 6,156.96
SRR6320854 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 5,679.20
SRR6320853 whole 6 week old aboral regenerate · regenerate 24hpa whole 6 week old aboral regenerate six weeks regenerate 24hpa SRP125570 5,428.34
SRR6320859 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 6,286.75
SRR6320860 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 5,517.31
SRR6320857 whole 6 week old aboral regenerate · regenerate 20hpa whole 6 week old aboral regenerate six weeks regenerate 20hpa SRP125570 5,195.43
SRR6320858 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 5,868.53
SRR6320881 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 5,797.36
SRR6320880 whole 6 week old aboral regenerate · regenerate 16hpa whole 6 week old aboral regenerate six weeks regenerate 16hpa SRP125570 5,587.78
SRR6320864 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 5,232.67
SRR6320862 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 5,161.64
SRR6320865 whole 6 week old aboral regenerate · regenerate 72hpa whole 6 week old aboral regenerate six weeks regenerate 72hpa SRP125570 4,715.80
SRR6320869 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 6,380.62
SRR6320867 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 5,368.82
SRR6320866 whole 6 week old aboral regenerate · regenerate 60hpa whole 6 week old aboral regenerate six weeks regenerate 60hpa SRP125570 5,024.96
SRR6320868 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 5,958.13
SRR6320870 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 5,155.18
SRR6320871 whole 6 week old aboral regenerate · regenerate 48hpa whole 6 week old aboral regenerate six weeks regenerate 48hpa SRP125570 5,079.45
SRR6320876 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 6,288.93
SRR6320875 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 6,030.44
SRR6320874 whole 6 week old aboral regenerate · regenerate 8hpa whole 6 week old aboral regenerate six weeks regenerate 8hpa SRP125570 5,830.33
SRR6320878 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 6,664.69
SRR6320879 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 6,552.59
SRR6320877 whole 6 week old aboral regenerate · regenerate 12hpa whole 6 week old aboral regenerate six weeks regenerate 12hpa SRP125570 5,659.62

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.

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 correlated36XP_001640566.10.97226531789555
Negatively correlated48XP_048590162.1-0.765397970477172

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 5 (0.702, 0.963%)
NVECT_bodywallbody wall with mesenteries · 6-8 weeks adults11,74213in viewerProgenitor (1.106, 0.969%)
Epidermis (0.771, 0.95%)
NVECT_embryoembryos · 8, 10 and 12 h after fertilisation (deposit labels 8h/10h/12h)9,71117in viewerCluster 16 (3.016, 0.986%)
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/organs2,53216in viewerCluster 3 (1.088, 0.973%)
Cluster 5 (0.925, 0.98%)
Cluster 10 (0.68, 0.961%)
Cluster 12 (0.727, 0.944%)
NVECT_nervousGastrula Cells · nervous system16,59027in viewerCluster 7 (0.71, 0.947%)
Cluster 24 (0.856, 0.926%)
NVECT_notch48hembryos treated 24-48 hpf (DMSO vs LY411575) · 48 hpf19,0447not in this dataset–
NVECT_tentacletentacle · Adult tissues/organs7,97719in viewerCluster 0 (0.584, 0.949%)
Cluster 1 (0.487, 0.927%)
Cluster 11 (0.582, 0.97%)

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-seqH3K27ac_gastrulae_24h2Promoter (1-2kb) 1 · Promoter (<=1kb) 1
H3K27ac_planulae_4days1Promoter (<=1kb) 1
H3K4me2_gastrulae_24h1Promoter (<=1kb) 1
H3K4me2_polyps1Promoter (<=1kb) 1
H3K4me3_gastrulae_24h1Promoter (<=1kb) 1
H3K4me3_planulae_4days1Promoter (<=1kb) 1
H3K4me3_polyps1Promoter (<=1kb) 1
H3K27ac_Ncol3_negative1Promoter (<=1kb) 1
H3K27ac_Ncol3_positive1Promoter (<=1kb) 1
H3K27ac_Nep3_negative1Promoter (<=1kb) 1
H3K36me3_gastrulae_24h1Promoter (<=1kb) 1
H3K36me3_planulae_4days1Promoter (<=1kb) 1
H3K36me3_polyps1Promoter (<=1kb) 1
H3K4me1_planulae_4days1Promoter (<=1kb) 1
H3K4me2_neuronal_ELAV_cells1Promoter (<=1kb) 1

2 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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