Detailed information of HSymV2.0_g06.10983_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_6:22657402...22671811
NR annotation: XP_047144551.1, calcium-activated potassium channel subunit alpha-1 [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
Q28204Calcium-activated potassium channel subunit alpha-1 OS=Bos taurus OX=9913 GN=KCNMA1 PE=1 SV=2
O18867Calcium-activated potassium channel subunit alpha-1 (Fragment) OS=Macaca mulatta OX=9544 GN=KCNMA1 PE=2 SV=1
O18866Calcium-activated potassium channel subunit alpha-1 (Fragment) OS=Sus scrofa OX=9823 GN=KCNMA1 PE=2 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001513 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03493
all species →		BK_channel_aCalcium-activated BK potassium channel alpha subunitFamilyInterproscan
PF07885
all species →		Ion_trans_2Ion channelFamilyInterproscan
PF21014
all species →		Slowpoke_CCa2+-activated K+ channel Slowpoke, TrkA_C like domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR003929
all species →		DomainCalcium-activated potassium channel BK, alpha subunitInterproscan
IPR027359
all species →		Homologous_superfamilyVoltage-dependent channel domain superfamilyInterproscan
IPR013099
all species →		DomainPotassium channel domainInterproscan
IPR047871
all species →		FamilyCalcium-activated potassium channel slowpoke-likeInterproscan
IPR048735
all species →		DomainCa2+-activated K+ channel Slowpoke-like, C-terminal domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10027
all species →		CALCIUM-ACTIVATED POTASSIUM CHANNEL ALPHA CHAINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006813
all species →		Biological Processpotassium ion transportInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0005267
all species →		Molecular Functionpotassium channel activityInterproscan
GO:0045211
all species →		Cellular Componentpostsynaptic membraneInterproscan
GO:0060072
all species →		Molecular Functionlarge conductance calcium-activated potassium channel activityInterproscan
GO:0071805
all species →		Biological Processpotassium ion transmembrane transportInterproscan

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
K04936KCNMA1, KCA1.1; potassium large conductance calcium-activated channel subfamily M alpha member 1-Ion channelsko04040deepkoala

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_g06.10983_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
42TPM > 0
3Conditions
51.8Max TPM
17.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole embryo 36 35 19.03 51.84
Whole embryo · Triptolide 20 uM 4 3 5.57 9.91
Whole embryo · DMSO 0.5% 4 4 11.09 14.82

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR24482160 Whole embryo Whole embryo 24 hpf not recorded SRP436676 51.84
SRR24482159 Whole embryo Whole embryo 24 hpf not recorded SRP436676 49.07
SRR24482157 Whole embryo Whole embryo 48 hpf not recorded SRP436676 41.01
SRR24482156 Whole embryo Whole embryo 72 hpf not recorded SRP436676 37.49
SRR24482155 Whole embryo Whole embryo 72 hpf not recorded SRP436676 28.93
SRR24482158 Whole embryo Whole embryo 48 hpf not recorded SRP436676 28.70
SRR24482134 Whole embryo Whole embryo 5 hpf not recorded SRP436676 20.81
SRR24482174 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 20.75
SRR24482173 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 19.08
SRR24482141 Whole embryo Whole embryo 1 hpf not recorded SRP436676 18.65
SRR24482172 Whole embryo Whole embryo 30 mpf not recorded SRP436676 18.34
SRR24482140 Whole embryo Whole embryo 2 hpf not recorded SRP436676 18.31
SRR24482145 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 18.10
SRR24482139 Whole embryo Whole embryo 2 hpf not recorded SRP436676 17.63
SRR24482133 Whole embryo Whole embryo 6 hpf not recorded SRP436676 17.44
SRR24482175 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 17.38
SRR24482143 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 17.34
SRR24482144 Whole embryo Whole embryo Unfertilized egg not recorded SRP436676 16.67
SRR24482176 Whole embryo Whole embryo 1 hpf not recorded SRP436676 16.54
SRR24482138 Whole embryo Whole embryo 3 hpf not recorded SRP436676 16.42
SRR24482161 Whole embryo Whole embryo 7 hpf not recorded SRP436676 16.28
SRR24482171 Whole embryo Whole embryo 1 hpf not recorded SRP436676 16.09
SRR24482136 Whole embryo Whole embryo 4 hpf not recorded SRP436676 15.39
SRR24482137 Whole embryo Whole embryo 3 hpf not recorded SRP436676 15.36
SRR24482169 Whole embryo Whole embryo 2 hpf not recorded SRP436676 14.75
SRR24482162 Whole embryo Whole embryo 7 hpf not recorded SRP436676 14.56
SRR24482135 Whole embryo Whole embryo 4 hpf not recorded SRP436676 13.52
SRR24482142 Whole embryo Whole embryo 30 mpf not recorded SRP436676 13.29
SRR24482168 Whole embryo Whole embryo 3 hpf not recorded SRP436676 12.45
SRR24482170 Whole embryo Whole embryo 2 hpf not recorded SRP436676 12.18
SRR24482153 Whole embryo Whole embryo 7 hpf not recorded SRP436676 11.41
SRR24482167 Whole embryo Whole embryo 3 hpf not recorded SRP436676 11.01
SRR24482163 Whole embryo Whole embryo 6 hpf not recorded SRP436676 10.29
SRR24482165 Whole embryo Whole embryo 4 hpf not recorded SRP436676 10.27
SRR24482166 Whole embryo Whole embryo 4 hpf not recorded SRP436676 7.90
SRR24482177 Whole embryo Whole embryo 1 hpf not recorded SRP436676 0.00
SRR24482150 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 9.91
SRR24482149 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 9.31
SRR24482147 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 3.05
SRR24482146 Whole embryo · Triptolide 20 uM Whole embryo 7 hpf Triptolide 20 uM SRP436676 0.00
SRR24482151 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 14.82
SRR24482152 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 12.71
SRR24482148 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 9.28
SRR24482154 Whole embryo · DMSO 0.5% Whole embryo 7 hpf DMSO 0.5% SRP436676 7.56

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 correlated12HSymV2.0_g04.06881_t10.935950406512289
Negatively correlated48HSymV2.0_g04.06101_t1-0.894880770374434

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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