Detailed information of XP_066923885.1 in Clytia hemisphaerica

Genomic Location: NW_027103993.1:97117...107775
NR annotation: XP_002161816.1, rab5 GDP/GTP exchange factor [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
O18973Rab5 GDP/GTP exchange factor OS=Bos taurus OX=9913 GN=RABGEF1 PE=1 SV=1
Q9UJ41Rab5 GDP/GTP exchange factor OS=Homo sapiens OX=9606 GN=RABGEF1 PE=1 SV=3
Q9JM13Rab5 GDP/GTP exchange factor OS=Mus musculus OX=10090 GN=Rabgef1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004081 (this species only) · gene tree & orthology
Ubiquitin familyUBD|ZnF|ZnF_A20 · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02204
all species →		VPS9Vacuolar sorting protein 9 (VPS9) domainFamilyInterproscan
PF01754
all species →		zf-A20A20-like zinc fingerFamilyInterproscan
PF18151
all species →		DUF5601Domain of unknown function (DUF5601)DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR002653
all species →		DomainZinc finger, A20-typeInterproscan
IPR003123
all species →		DomainVPS9 domainInterproscan
IPR037191
all species →		Homologous_superfamilyVPS9 domain superfamilyInterproscan
IPR045046
all species →		FamilyVacuolar protein sorting-associated protein 9-likeInterproscan
IPR041545
all species →		DomainRABX5, catalytic core helical domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23101
all species →		RAB GDP/GTP EXCHANGE FACTORInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0008270
all species →		Molecular Functionzinc ion bindingInterproscan
GO:0005085
all species →		Molecular Functionguanyl-nucleotide exchange factor activityInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0016192
all species →		Biological Processvesicle-mediated transportInterproscan
GO:0030139
all species →		Cellular Componentendocytic vesicleInterproscan
GO:0031267
all species →		Molecular Functionsmall GTPase bindingInterproscan

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
K20131RABGEF1; Rab5 GDP/GTP exchange factor-Membrane traffickingko04131deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_066923885.1 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
17.4Max TPM
12.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Mature medusa 5 5 14.97 17.35
medusa · Experiment Condition A1 4 4 8.05 9.04
medusa · Experiment Condition A2 4 4 8.47 10.02
medusa · Experiment Condition A3 4 4 13.79 15.08
Early gastrula 2 2 16.28 17.39
Planula 24hpf 2 2 13.39 13.43
Planula 48hpf 2 2 10.79 11.24
Planula 72hpf 2 2 10.70 12.59
Primary polyp 2 2 9.64 9.91
Gastrozooid 2 2 13.00 13.49
Gonozooid 2 2 12.28 12.30
Stolon 2 2 10.05 10.74
Baby medusa 2 2 14.41 14.42
medusa · Experiment Condition B1 2 2 16.60 16.77
medusa · Experiment Condition B2 2 2 9.89 10.08
Mixed 1 1 10.45 10.45

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 17.35
ERR2862245 Mature medusa not recorded Mature medusa not recorded ERP110164 17.11
ERR2816250 Mature medusa not recorded Mature medusa not recorded ERP110164 14.91
ERR2816249 Mature medusa not recorded Mature medusa not recorded ERP110164 13.05
ERR2816248 Mature medusa not recorded Mature medusa not recorded ERP110164 12.45
ERR3299476 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 9.04
ERR3299475 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 8.72
ERR3299477 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 7.88
ERR3299478 medusa · Experiment Condition A1 not recorded medusa Experiment Condition A1 ERP115020 6.55
ERR3299479 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 10.02
ERR3299480 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 9.56
ERR3299481 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 7.53
ERR3299482 medusa · Experiment Condition A2 not recorded medusa Experiment Condition A2 ERP115020 6.75
ERR3299484 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 15.08
ERR3299483 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 14.01
ERR3299485 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 13.16
ERR3299486 medusa · Experiment Condition A3 not recorded medusa Experiment Condition A3 ERP115020 12.92
ERR2816230 Early gastrula not recorded Early gastrula not recorded ERP110164 17.39
ERR2816231 Early gastrula not recorded Early gastrula not recorded ERP110164 15.17
ERR2816232 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 13.43
ERR2816233 Planula 24hpf not recorded Planula 24hpf not recorded ERP110164 13.35
ERR2816235 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 11.24
ERR2816234 Planula 48hpf not recorded Planula 48hpf not recorded ERP110164 10.34
ERR2816236 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 12.59
ERR2816237 Planula 72hpf not recorded Planula 72hpf not recorded ERP110164 8.81
ERR2816238 Primary polyp not recorded Primary polyp not recorded ERP110164 9.91
ERR2816239 Primary polyp not recorded Primary polyp not recorded ERP110164 9.38
ERR2816240 Gastrozooid not recorded Gastrozooid not recorded ERP110164 13.49
ERR2816241 Gastrozooid not recorded Gastrozooid not recorded ERP110164 12.51
ERR2816243 Gonozooid not recorded Gonozooid not recorded ERP110164 12.30
ERR2816242 Gonozooid not recorded Gonozooid not recorded ERP110164 12.26
ERR2816245 Stolon not recorded Stolon not recorded ERP110164 10.74
ERR2816244 Stolon not recorded Stolon not recorded ERP110164 9.37
ERR2816246 Baby medusa not recorded Baby medusa not recorded ERP110164 14.42
ERR2816247 Baby medusa not recorded Baby medusa not recorded ERP110164 14.39
ERR3299471 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 16.77
ERR3299472 medusa · Experiment Condition B1 not recorded medusa Experiment Condition B1 ERP115020 16.44
ERR3299473 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 10.08
ERR3299474 medusa · Experiment Condition B2 not recorded medusa Experiment Condition B2 ERP115020 9.70
ERR2862244 Mixed not recorded Mixed not recorded ERP110164 10.45

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 correlated24XP_066930625.10.833641793624976
Negatively correlated35XP_066931312.1-0.780920641994518

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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