Detailed information of HSymV2.0_g12.21871_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_12:20954333...20963813
NR annotation: XP_047135944.1, probable citrate synthase 2, mitochondrial [Hydra vulgaris]
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
Q17GM7Probable citrate synthase 1, mitochondrial OS=Aedes aegypti OX=7159 GN=AAEL002956 PE=3 SV=1
Q16P20Probable citrate synthase 2, mitochondrial OS=Aedes aegypti OX=7159 GN=AAEL011789 PE=3 SV=1
Q0QHL3Probable citrate synthase, mitochondrial OS=Glossina morsitans morsitans OX=37546 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004182 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00285
all species →		Citrate_syntCitrate synthase, C-terminal domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR016143
all species →		Homologous_superfamilyCitrate synthase-like, small alpha subdomainInterproscan
IPR010109
all species →		FamilyCitrate synthase, eukaryotic-typeInterproscan
IPR036969
all species →		Homologous_superfamilyCitrate synthase superfamilyInterproscan
IPR032675
all species →		Homologous_superfamilyLeucine-rich repeat domain superfamilyInterproscan
IPR002020
all species →		FamilyCitrate synthaseInterproscan
IPR019810
all species →		Active_siteCitrate synthase active siteInterproscan
IPR016142
all species →		Homologous_superfamilyCitrate synthase-like, large alpha subdomainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11739
all species →		CITRATE SYNTHASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004108
all species →		Molecular Functioncitrate (Si)-synthase activityInterproscan
GO:0006099
all species →		Biological Processtricarboxylic acid cycleInterproscan
GO:0006101
all species →		Biological Processcitrate metabolic processInterproscan
GO:0046912
all species →		Molecular Functionacyltransferase activity, acyl groups converted into alkyl on transferInterproscan
GO:0005759
all species →		Cellular Componentmitochondrial matrixInterproscan
GO:0005975
all species →		Biological Processcarbohydrate 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 HSymV2.0_g12.21871_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_g12.21871_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
253.0Max TPM
181.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 36 183.70 252.95
Whole embryo · Triptolide 20 uM 4 4 167.80 186.22
Whole embryo · DMSO 0.5% 4 4 171.22 184.92

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 252.95
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 247.86
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 245.52
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 228.99
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 226.85
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 224.89
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 221.90
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 219.63
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 218.38
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 215.92
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 215.16
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 211.95
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 211.53
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 204.81
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 204.45
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 200.64
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 195.02
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 193.89
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 193.78
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 186.81
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 185.00
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 175.63
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 174.03
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 173.13
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 167.55
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 167.32
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 165.58
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 160.30
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 158.99
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 156.60
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 126.88
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 126.07
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 106.19
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 99.76
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 85.87
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 63.32
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 186.22
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 185.82
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 153.56
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 145.61
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 184.92
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 178.94
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 167.98
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 153.05

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 correlated10HSymV2.0_g05.08553_t10.915819750925651
Negatively correlated12HSymV2.0_g13.22466_t1-0.864207314085584

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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