Detailed information of XP_066932981.1 in Clytia hemisphaerica

Genomic Location: NW_027104433.1:910060...918559
NR annotation: XP_002164804.2, succinate dehydrogenase cytochrome b560 subunit, mitochondrial [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P70097Succinate dehydrogenase cytochrome b560 subunit, mitochondrial OS=Cricetulus griseus OX=10029 GN=SDHC PE=2 SV=1
Q9CZB0Succinate dehydrogenase cytochrome b560 subunit, mitochondrial OS=Mus musculus OX=10090 GN=Sdhc PE=1 SV=1
D0VWV4Succinate dehydrogenase cytochrome b560 subunit, mitochondrial OS=Sus scrofa OX=9823 GN=SDHC PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007104 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01127
all species →		Sdh_cytSuccinate dehydrogenase/Fumarate reductase transmembrane subunitFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR034804
all species →		Homologous_superfamilyFumarate reductase/succinate dehydrogenase, transmembrane subunitInterproscan
IPR000701
all species →		FamilySuccinate dehydrogenase/fumarate reductase type B, transmembrane subunitInterproscan
IPR018495
all species →		Conserved_siteSuccinate dehydrogenase, cytochrome b subunit, conserved siteInterproscan
IPR014314
all species →		FamilySuccinate dehydrogenase, cytochrome b556 subunitInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10978
all species →		SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNITInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0006099
all species →		Biological Processtricarboxylic acid cycleInterproscan
GO:0009055
all species →		Molecular Functionelectron transfer activityInterproscan
GO:0005749
all species →		Cellular Componentobsolete mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)Interproscan
GO:0006121
all species →		Biological Processmitochondrial electron transport, succinate to ubiquinoneInterproscan
GO:0045281
all species →		Cellular Componentobsolete succinate dehydrogenase complexInterproscan

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
K00236SDHC, SDH3; succinate dehydrogenase (ubiquinone) cytochrome b560 subunit-Non-alcoholic fatty liver diseaseko04932deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_066932981.1 across 40 RNA-seq samples of Clytia hemisphaerica. 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.

40Samples
40TPM > 0
16Conditions
234.3Max TPM
137.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Mature medusa 5 5 140.06 178.85
medusa · Experiment Condition A1 4 4 133.37 142.21
medusa · Experiment Condition A2 4 4 84.24 86.62
medusa · Experiment Condition A3 4 4 29.75 33.14
Early gastrula 2 2 96.96 102.59
Planula 24hpf 2 2 129.49 131.14
Planula 48hpf 2 2 184.81 199.05
Planula 72hpf 2 2 230.62 232.58
Primary polyp 2 2 220.99 232.08
Gastrozooid 2 2 102.71 105.36
Gonozooid 2 2 231.84 234.32
Stolon 2 2 186.42 190.83
Baby medusa 2 2 192.96 199.29
medusa · Experiment Condition B1 2 2 125.08 130.45
medusa · Experiment Condition B2 2 2 123.57 125.40
Mixed 1 1 158.79 158.79

Per sample · hover a bar for the full sample record

Show the sample table (40 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR2816251 Mature medusa not recorded Mature medusa not recorded ERP110164 178.85
ERR2816250 Mature medusa not recorded Mature medusa not recorded ERP110164 177.14
ERR2816248 Mature medusa not recorded Mature medusa not recorded ERP110164 129.76
ERR2816249 Mature medusa not recorded Mature medusa not recorded ERP110164 129.49
ERR2862245 Mature medusa not recorded Mature medusa not recorded ERP110164 85.09
ERR3299476 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 142.21
ERR3299477 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 132.18
ERR3299475 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 130.82
ERR3299478 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 128.27
ERR3299481 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 86.62
ERR3299480 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 85.09
ERR3299482 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 83.09
ERR3299479 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 82.17
ERR3299486 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 33.14
ERR3299484 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 32.06
ERR3299483 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 27.25
ERR3299485 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 26.56
ERR2816230 Early gastrula not recorded Early gastrula not recorded ERP110164 102.59
ERR2816231 Early gastrula not recorded Early gastrula not recorded ERP110164 91.32
ERR2816233 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 131.14
ERR2816232 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 127.84
ERR2816234 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 199.05
ERR2816235 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 170.56
ERR2816237 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 232.58
ERR2816236 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 228.67
ERR2816239 Primary polyp not recorded Primary polyp not recorded ERP110164 232.08
ERR2816238 Primary polyp not recorded Primary polyp not recorded ERP110164 209.90
ERR2816240 Gastrozooid not recorded Gastrozooid not recorded ERP110164 105.36
ERR2816241 Gastrozooid not recorded Gastrozooid not recorded ERP110164 100.05
ERR2816243 Gonozooid not recorded Gonozooid not recorded ERP110164 234.32
ERR2816242 Gonozooid not recorded Gonozooid not recorded ERP110164 229.35
ERR2816244 Stolon not recorded Stolon not recorded ERP110164 190.83
ERR2816245 Stolon not recorded Stolon not recorded ERP110164 182.02
ERR2816246 Baby medusa not recorded Baby medusa not recorded ERP110164 199.29
ERR2816247 Baby medusa not recorded Baby medusa not recorded ERP110164 186.62
ERR3299471 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 130.45
ERR3299472 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 119.71
ERR3299474 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 125.40
ERR3299473 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 121.73
ERR2862244 Mixed not recorded Mixed not recorded ERP110164 158.79

Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM, StringTie quantification over 40 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 Clytia hemisphaerica 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_066919858.10.933809992773832
Negatively correlated25XP_066923979.1-0.843197889716987

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 Clytia hemisphaerica, 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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