Detailed information of XP_065661818.1 in Hydra vulgaris

Genomic Location: NC_088928.1:41821188...41855049
NR annotation: XP_047133170.1, mitochondrial import inner membrane translocase subunit TIM50 [Hydra vulgaris]
Species Hydra vulgaris · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q6NWD4Mitochondrial import inner membrane translocase subunit TIM50 OS=Danio rerio OX=7955 GN=timm50 PE=2 SV=2
Q3ZCQ8Mitochondrial import inner membrane translocase subunit TIM50 OS=Homo sapiens OX=9606 GN=TIMM50 PE=1 SV=2
Q22647Mitochondrial import inner membrane translocase subunit TIM50 OS=Caenorhabditis elegans OX=6239 GN=scpl-4 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006655 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03031
all species →		NIFNLI interacting factor-like phosphataseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR004274
all species →		DomainFCP1 homology domainInterproscan
IPR036412
all species →		Homologous_superfamilyHAD-like superfamilyInterproscan
IPR050365
all species →		FamilyMitochondrial import inner membrane translocase subunit TIM50Interproscan
IPR023214
all species →		Homologous_superfamilyHAD superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12210
all species →		DULLARD PROTEIN PHOSPHATASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005744
all species →		Cellular ComponentTIM23 mitochondrial import inner membrane translocase complexInterproscan
GO:0030150
all species →		Biological Processprotein import into mitochondrial matrixInterproscan

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
K17496TIM50; mitochondrial import inner membrane translocase subunit TIM50-Transportersko02000deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_065661818.1 across 60 RNA-seq samples of Hydra vulgaris. 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.

60Samples
60TPM > 0
8Conditions
52.4Max TPM
43.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Regenerating head · dmso treatment 18 18 44.85 52.44
Regenerating head · 25uM U0126 treatment 15 15 44.25 52.44
Regenerating foot · dmso treatment 9 9 43.56 47.95
Regenerating foot · 25uM U0126 treatment 8 8 40.40 50.05
Regenerating head · u0126 treatment 3 3 40.69 41.20
Whole animal · 25uM U0126 treatment 3 3 44.55 50.32
Whole animal · dmso treatment 3 3 44.87 52.28
Regenerating foot · u0126 treatment 1 1 41.81 41.81

Per sample · hover a bar for the full sample record

Show the sample table (60 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR36435286 Regenerating head · dmso treatment Regenerating head 0hpa dmso treatment SRP654941 52.44
SRR36435284 Regenerating head · dmso treatment Regenerating head 0hpa dmso treatment SRP654941 51.89
SRR36435305 Regenerating head · dmso treatment Regenerating head 1.5hpa dmso treatment SRP654941 51.77
SRR36435285 Regenerating head · dmso treatment Regenerating head 0hpa dmso treatment SRP654941 50.92
SRR36435313 Regenerating head · dmso treatment Regenerating head 0hpa dmso treatment SRP654941 50.39
SRR36435304 Regenerating head · dmso treatment Regenerating head 1.5hpa dmso treatment SRP654941 48.72
SRR36435310 Regenerating head · dmso treatment Regenerating head 0hpa dmso treatment SRP654941 47.35
SRR36435277 Regenerating head · dmso treatment Regenerating head 8hpa dmso treatment SRP654941 44.96
SRR36435279 Regenerating head · dmso treatment Regenerating head 8hpa dmso treatment SRP654941 44.29
SRR36435272 Regenerating head · dmso treatment Regenerating head 12hpa dmso treatment SRP654941 43.41
SRR36435306 Regenerating head · dmso treatment Regenerating head 1.5hpa dmso treatment SRP654941 43.07
SRR36435271 Regenerating head · dmso treatment Regenerating head 12hpa dmso treatment SRP654941 42.88
SRR36435280 Regenerating head · dmso treatment Regenerating head 8hpa dmso treatment SRP654941 41.09
SRR36435273 Regenerating head · dmso treatment Regenerating head 12hpa dmso treatment SRP654941 41.05
SRR36435307 Regenerating head · dmso treatment Regenerating head 3hpa dmso treatment SRP654941 40.79
SRR36435309 Regenerating head · dmso treatment Regenerating head 3hpa dmso treatment SRP654941 39.40
SRR36435308 Regenerating head · dmso treatment Regenerating head 3hpa dmso treatment SRP654941 37.68
SRR36435312 Regenerating head · dmso treatment Regenerating head 0hpa dmso treatment SRP654941 35.19
SRR36435281 Regenerating head · 25uM U0126 treatment Regenerating head 0hpa 25uM U0126 treatment SRP654941 52.44
SRR36435303 Regenerating head · 25uM U0126 treatment Regenerating head 0hpa 25uM U0126 treatment SRP654941 49.25
SRR36435282 Regenerating head · 25uM U0126 treatment Regenerating head 0hpa 25uM U0126 treatment SRP654941 47.66
SRR36435302 Regenerating head · 25uM U0126 treatment Regenerating head 0hpa 25uM U0126 treatment SRP654941 47.04
SRR36435274 Regenerating head · 25uM U0126 treatment Regenerating head 8hpa 25uM U0126 treatment SRP654941 45.82
SRR36435296 Regenerating head · 25uM U0126 treatment Regenerating head 1.5hpa 25uM U0126 treatment SRP654941 45.44
SRR36435295 Regenerating head · 25uM U0126 treatment Regenerating head 1.5hpa 25uM U0126 treatment SRP654941 45.34
SRR36435299 Regenerating head · 25uM U0126 treatment Regenerating head 3hpa 25uM U0126 treatment SRP654941 44.14
SRR36435301 Regenerating head · 25uM U0126 treatment Regenerating head 0hpa 25uM U0126 treatment SRP654941 42.19
SRR36435297 Regenerating head · 25uM U0126 treatment Regenerating head 3hpa 25uM U0126 treatment SRP654941 42.12
SRR36435294 Regenerating head · 25uM U0126 treatment Regenerating head 1.5hpa 25uM U0126 treatment SRP654941 42.11
SRR36435283 Regenerating head · 25uM U0126 treatment Regenerating head 0hpa 25uM U0126 treatment SRP654941 41.95
SRR36435298 Regenerating head · 25uM U0126 treatment Regenerating head 3hpa 25uM U0126 treatment SRP654941 41.73
SRR36435276 Regenerating head · 25uM U0126 treatment Regenerating head 8hpa 25uM U0126 treatment SRP654941 39.91
SRR36435275 Regenerating head · 25uM U0126 treatment Regenerating head 8hpa 25uM U0126 treatment SRP654941 36.55
SRR36435265 Regenerating foot · dmso treatment Regenerating foot 1.5hpa dmso treatment SRP654941 47.95
SRR36435323 Regenerating foot · dmso treatment Regenerating foot 0hpa dmso treatment SRP654941 47.03
SRR36435322 Regenerating foot · dmso treatment Regenerating foot 0hpa dmso treatment SRP654941 46.67
SRR36435266 Regenerating foot · dmso treatment Regenerating foot 1.5hpa dmso treatment SRP654941 43.65
SRR36435289 Regenerating foot · dmso treatment Regenerating foot 3hpa dmso treatment SRP654941 43.63
SRR36435278 Regenerating foot · dmso treatment Regenerating foot 3hpa dmso treatment SRP654941 42.42
SRR36435311 Regenerating foot · dmso treatment Regenerating foot 0hpa dmso treatment SRP654941 42.12
SRR36435300 Regenerating foot · dmso treatment Regenerating foot 3hpa dmso treatment SRP654941 41.38
SRR36435267 Regenerating foot · dmso treatment Regenerating foot 1.5hpa dmso treatment SRP654941 37.20
SRR36435321 Regenerating foot · 25uM U0126 treatment Regenerating foot 0hpa 25uM U0126 treatment SRP654941 50.05
SRR36435314 Regenerating foot · 25uM U0126 treatment Regenerating foot 1.5hpa 25uM U0126 treatment SRP654941 44.32
SRR36435318 Regenerating foot · 25uM U0126 treatment Regenerating foot 3hpa 25uM U0126 treatment SRP654941 43.10
SRR36435320 Regenerating foot · 25uM U0126 treatment Regenerating foot 0hpa 25uM U0126 treatment SRP654941 40.66
SRR36435315 Regenerating foot · 25uM U0126 treatment Regenerating foot 1.5hpa 25uM U0126 treatment SRP654941 36.96
SRR36435316 Regenerating foot · 25uM U0126 treatment Regenerating foot 1.5hpa 25uM U0126 treatment SRP654941 36.58
SRR36435319 Regenerating foot · 25uM U0126 treatment Regenerating foot 3hpa 25uM U0126 treatment SRP654941 35.83
SRR36435317 Regenerating foot · 25uM U0126 treatment Regenerating foot 3hpa 25uM U0126 treatment SRP654941 35.69
SRR36435268 Regenerating head · u0126 treatment Regenerating head 12hpa u0126 treatment SRP654941 41.20
SRR36435269 Regenerating head · u0126 treatment Regenerating head 12hpa u0126 treatment SRP654941 40.57
SRR36435270 Regenerating head · u0126 treatment Regenerating head 12hpa u0126 treatment SRP654941 40.32
SRR36435288 Whole animal · 25uM U0126 treatment Whole animal 12h 25uM U0126 treatment SRP654941 50.32
SRR36435290 Whole animal · 25uM U0126 treatment Whole animal 12h 25uM U0126 treatment SRP654941 44.61
SRR36435287 Whole animal · 25uM U0126 treatment Whole animal 12h 25uM U0126 treatment SRP654941 38.73
SRR36435292 Whole animal · dmso treatment Whole animal 12h dmso treatment SRP654941 52.28
SRR36435293 Whole animal · dmso treatment Whole animal 12h dmso treatment SRP654941 42.38
SRR36435291 Whole animal · dmso treatment Whole animal 12h dmso treatment SRP654941 39.97
SRR36435264 Regenerating foot · u0126 treatment Regenerating foot 0hpa u0126 treatment SRP654941 41.81

Source: CnidoSite RNA-seq expression matrices (HVULG_TPM, StringTie quantification over 60 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 Hydra vulgaris 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 correlated1XP_065646602.10.703246531990079
Negatively correlated5XP_065653506.1-0.619365015979449

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 Hydra vulgaris, 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.

DatasetTissue / stageCellsCell typesThis geneMarker of
HVULG_siebert_atlasWhole animals · Adult (whole animal)25,43842not in this dataset–

A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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.

Peak calls overlapping this gene

AssaySamplePeaksRegion
ChIP-seqH3K27ac_regenerating_head_0hr1Promoter (<=1kb) 1
H3K4me2_wholeAnimal1Promoter (<=1kb) 1
H3K4me3_head1Promoter (<=1kb) 1
H3K4me3_regenerating_head_0hr1Promoter (<=1kb) 1
H3K4me3_regenerating_head_24hr1Promoter (<=1kb) 1
H3K4me3_regenerating_head_6hr1Promoter (<=1kb) 1
H4K20me1_whole_polyp_ALP_treated1Intron 1

Browse the full epigenomic landscape of this species: ChIP-seq.

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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