Detailed information of BRAKERKREP00000003257.1 in Hydra viridissima

Genomic Location: QPEY01000009.1:1829181...1830973
NR annotation: XP_002170766.1, lysosomal-associated transmembrane protein 4B [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q91XQ6Lysosomal-associated transmembrane protein 4B OS=Mus musculus OX=10090 GN=Laptm4b PE=2 SV=1
Q5U1W4Lysosomal-associated transmembrane protein 4B OS=Rattus norvegicus OX=10116 GN=Laptm4b PE=2 SV=1
Q5ZML7Lysosomal-associated transmembrane protein 4A OS=Gallus gallus OX=9031 GN=LAPTM4A PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008341 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03821
all species →		MtpGolgi 4-transmembrane spanning transporterFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR051115
all species →		FamilyLysosomal-associated transmembrane transporterInterproscan
IPR004687
all species →		FamilyLysosomal-associated transmembrane protein 4/5Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12479
all species →		LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005765
all species →		Cellular Componentlysosomal membraneInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan

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
K12387LAPTM; lysosomal-associated transmembrane protein-Lysosomeko04142deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000003257.1 across 29 RNA-seq samples of Hydra viridissima. 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.

29Samples
10TPM > 0
7Conditions
11.6Max TPM
2.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole body 18 2 0.68 8.00
Whole 6 5 7.87 11.57
aposymbioic hydra M9 strain · aposymbioic hydra rep1 1 1 7.62 7.62
aposymbioic hydra M9 strain · aposymbioic hydra rep2 1 1 7.03 7.03
symbioic hydra M9 strain · symbioic hydra rep1 1 1 3.97 3.97
symbioic hydra M9 strain · symbioic hydra rep2 1 0 0.00 0.00
unannotated 1 0 0.00 0.00

Per sample · hover a bar for the full sample record

Show the sample table (29 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR21134060 whole body whole body not recorded not recorded SRP392977 8.00
SRR21134064 whole body whole body not recorded not recorded SRP392977 4.20
SRR21134050 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134051 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134052 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134053 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134054 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134055 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134056 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134057 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134058 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134059 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134061 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134062 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134063 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134065 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134066 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134067 whole body whole body not recorded not recorded SRP392977 0.00
SRR10058804 Whole Whole not recorded not recorded SRP220397 11.57
SRR10058803 Whole Whole not recorded not recorded SRP220397 10.50
SRR10058805 Whole Whole not recorded not recorded SRP220397 10.29
SRR10058806 Whole Whole not recorded not recorded SRP220397 7.92
SRR10058807 Whole Whole not recorded not recorded SRP220397 6.93
SRR10058802 Whole Whole not recorded not recorded SRP220397 0.00
DRR048593 aposymbioic hydra M9 strain · aposymbioic hydra rep1 not recorded not recorded aposymbioic hydra rep1 DRP003902 7.62
DRR048594 aposymbioic hydra M9 strain · aposymbioic hydra rep2 not recorded not recorded aposymbioic hydra rep2 DRP003902 7.03
DRR048595 symbioic hydra M9 strain · symbioic hydra rep1 not recorded not recorded symbioic hydra rep1 DRP003902 3.97
DRR048596 symbioic hydra M9 strain · symbioic hydra rep2 not recorded not recorded symbioic hydra rep2 DRP003902 0.00
ERR13389755 unannotated not recorded not recorded not recorded ERP162636 0.00

Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM, StringTie quantification over 29 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 viridissima 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 correlated8BRAKERKREP00000006381.10.989501274916728
Negatively correlated3BRAKERKREP00000024112.1-0.665811290957267

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 viridissima, 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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