Detailed information of HSymV2.0_g11.19590_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_11:9158406...9167877
NR annotation: XP_047133065.1, cysteine desulfurase, 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
Q9VKD3Cysteine desulfurase, mitochondrial OS=Drosophila melanogaster OX=7227 GN=Nfs1 PE=1 SV=1
Q5RDE7Cysteine desulfurase OS=Pongo abelii OX=9601 GN=NFS1 PE=2 SV=1
Q9Y697Cysteine desulfurase OS=Homo sapiens OX=9606 GN=NFS1 PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001536 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00266
all species →		Aminotran_5Aminotransferase class-VDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR015422
all species →		Homologous_superfamilyPyridoxal phosphate-dependent transferase, small domainInterproscan
IPR015424
all species →		Homologous_superfamilyPyridoxal phosphate-dependent transferaseInterproscan
IPR000192
all species →		DomainAminotransferase class V domainInterproscan
IPR020578
all species →		Binding_siteAminotransferase class-V, pyridoxal-phosphate binding siteInterproscan
IPR010240
all species →		FamilyCysteine desulfurase IscSInterproscan
IPR015421
all species →		Homologous_superfamilyPyridoxal phosphate-dependent transferase, major domainInterproscan
IPR016454
all species →		FamilyCysteine desulfuraseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11601
all species →		CYSTEINE DESULFURYLASE FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0030170
all species →		Molecular Functionpyridoxal phosphate bindingInterproscan
GO:0031071
all species →		Molecular Functioncysteine desulfurase activityInterproscan
GO:0044571
all species →		Biological Process[2Fe-2S] cluster assemblyInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0005739
all species →		Cellular ComponentmitochondrionInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0016226
all species →		Biological Processiron-sulfur cluster assemblyInterproscan

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
K04487iscS, NFS1; cysteine desulfuraseEC:2.8.1.7
Prokaryotic defense systemko02048deepkoala

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_g11.19590_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
43TPM > 0
3Conditions
172.5Max TPM
106.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 35 100.40 135.86
Whole embryo · Triptolide 20 uM 4 4 147.07 172.49
Whole embryo · DMSO 0.5% 4 4 122.30 143.78

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 135.86
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 135.65
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 135.57
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 135.20
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 134.55
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 131.31
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 130.06
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 128.79
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 128.23
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 127.20
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 127.16
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 125.35
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 124.75
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 121.63
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 113.34
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 111.77
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 110.98
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 108.64
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 108.13
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 106.27
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 105.27
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 102.35
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 100.93
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 98.78
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 96.41
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 94.19
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 90.76
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 84.12
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 82.85
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 54.12
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 51.00
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 48.60
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 47.17
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 45.24
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 32.06
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 0.00
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 172.49
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 159.82
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 128.67
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 127.29
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 143.78
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 138.51
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 113.33
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 93.57

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 correlated40HSymV2.0_g08.14776_t10.971744466997238
Negatively correlated9HSymV2.0_g04.06884_t1-0.877571361304841

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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