Detailed information of HSymV2.0_g14.24166_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_14:8578421...8601855
NR annotation: CAA08791.1, ribosomal protein L18a, partial [Podocoryna carnea]
Species Hydractinia symbiolongicarpus · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q7ZWJ4Large ribosomal subunit protein eL20 OS=Danio rerio OX=7955 GN=rpl18a PE=1 SV=1
G1TTY7Large ribosomal subunit protein eL20 OS=Oryctolagus cuniculus OX=9986 GN=RPL18A PE=1 SV=2
Q3T003Large ribosomal subunit protein eL20 OS=Bos taurus OX=9913 GN=RPL18A PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007044 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01400
all species →		AstacinAstacin (Peptidase family M12A)DomainInterproscan
PF01775
all species →		Ribosomal_L18ARibosomal proteins 50S-L18Ae/60S-L20/60S-L18ADomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001506
all species →		DomainPeptidase M12AInterproscan
IPR028877
all species →		FamilyLarge ribosomal subunit protein eL20Interproscan
IPR006026
all species →		DomainPeptidase, metallopeptidaseInterproscan
IPR024079
all species →		Homologous_superfamilyMetallopeptidase, catalytic domain superfamilyInterproscan
IPR021138
all species →		FamilyLarge ribosomal subunit protein eL20, eukaryotesInterproscan
IPR023573
all species →		DomainLarge ribosomal subunit protein eL20 domainInterproscan
IPR034035
all species →		DomainAstacin-like metallopeptidase domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10052
all species →		60S RIBOSOMAL PROTEIN L18AInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004222
all species →		Molecular Functionmetalloendopeptidase activityInterproscan
GO:0006508
all species →		Biological ProcessproteolysisInterproscan
GO:0008237
all species →		Molecular Functionmetallopeptidase activityInterproscan
GO:0008270
all species →		Molecular Functionzinc ion bindingInterproscan
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

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 HSymV2.0_g14.24166_t1.

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

Expression pattern (RNA-seq)

Transcript abundance of HSymV2.0_g14.24166_t1 across 44 RNA-seq samples of Hydractinia symbiolongicarpus. 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.

44Samples
44TPM > 0
3Conditions
1,669.5Max TPM
323.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 341.17 1,669.53
Whole embryo · Triptolide 20 uM 4 4 228.24 298.60
Whole embryo · DMSO 0.5% 4 4 261.34 331.98

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 1,669.53
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 1,603.91
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 1,151.07
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 1,036.63
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 814.65
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 665.46
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 312.65
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 312.03
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 269.84
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 226.06
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 218.50
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 213.40
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 205.75
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 202.41
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 194.50
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 193.96
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 190.55
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 190.17
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 189.78
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 185.99
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 180.32
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 174.15
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 172.60
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 142.04
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 140.15
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 139.65
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 136.07
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 134.93
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 132.86
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 132.55
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 129.45
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 127.54
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 127.49
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 125.67
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 120.63
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 119.24
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 298.60
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 265.77
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 183.23
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 165.37
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 331.98
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 304.11
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 211.64
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 197.62

Source: CnidoSite RNA-seq expression matrices (HSYMB_TPM, StringTie quantification over 44 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 Hydractinia symbiolongicarpus 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 correlated48HSymV2.0_g11.20325_t10.999218273204354
Negatively correlated5HSymV2.0_g05.09506_t1-0.940457594155493

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 Hydractinia symbiolongicarpus, 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.

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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