Detailed information of BRAKERKREP00000004569.1 in Hydra viridissima

Genomic Location: QPEY01000014.1:419622...435103
NR annotation: XP_047122687.1, solute carrier family 41 member 1 isoform X3 [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
Q8IVJ1Solute carrier family 41 member 1 OS=Homo sapiens OX=9606 GN=SLC41A1 PE=1 SV=2
Q5R839Solute carrier family 41 member 1 OS=Pongo abelii OX=9601 GN=SLC41A1 PE=2 SV=1
Q8BJA2Solute carrier family 41 member 1 OS=Mus musculus OX=10090 GN=Slc41a1 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006332 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01769
all species →		MgtEDivalent cation transporterFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR006667
all species →		DomainSLC41A/MgtE, integral membrane domainInterproscan
IPR036739
all species →		Homologous_superfamilySLC41A/MgtE divalent cation transporters, integral membrane domain superfamilyInterproscan
IPR045349
all species →		FamilySLC41A divalent cation transporterInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR16228
all species →		DIVALENT CATION TRANSPORTER SOLUTE CARRIER FAMILY 41Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006812
all species →		Biological Processmonoatomic cation transportInterproscan
GO:0008324
all species →		Molecular Functionmonoatomic cation transmembrane transporter activityInterproscan
GO:0005886
all species →		Cellular Componentplasma membraneInterproscan

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
K15122SLC41A; solute carrier family 41-Transportersko02000deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000004569.1 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
18TPM > 0
7Conditions
139.2Max TPM
22.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole body 18 9 25.82 139.17
Whole 6 6 22.31 26.24
aposymbioic hydra M9 strain · aposymbioic hydra rep1 1 1 21.94 21.94
aposymbioic hydra M9 strain · aposymbioic hydra rep2 1 1 15.60 15.60
symbioic hydra M9 strain · symbioic hydra rep1 1 1 10.05 10.05
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
SRR21134055 whole body whole body not recorded not recorded SRP392977 139.17
SRR21134056 whole body whole body not recorded not recorded SRP392977 105.57
SRR21134059 whole body whole body not recorded not recorded SRP392977 60.64
SRR21134054 whole body whole body not recorded not recorded SRP392977 36.67
SRR21134057 whole body whole body not recorded not recorded SRP392977 29.15
SRR21134051 whole body whole body not recorded not recorded SRP392977 27.64
SRR21134064 whole body whole body not recorded not recorded SRP392977 23.80
SRR21134060 whole body whole body not recorded not recorded SRP392977 23.09
SRR21134050 whole body whole body not recorded not recorded SRP392977 19.04
SRR21134052 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134053 whole body whole body not recorded not recorded SRP392977 0.00
SRR21134058 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
SRR10058802 Whole Whole not recorded not recorded SRP220397 26.24
SRR10058804 Whole Whole not recorded not recorded SRP220397 25.14
SRR10058807 Whole Whole not recorded not recorded SRP220397 23.39
SRR10058806 Whole Whole not recorded not recorded SRP220397 20.99
SRR10058803 Whole Whole not recorded not recorded SRP220397 20.04
SRR10058805 Whole Whole not recorded not recorded SRP220397 18.06
DRR048593 aposymbioic hydra M9 strain · aposymbioic hydra rep1 not recorded not recorded aposymbioic hydra rep1 DRP003902 21.94
DRR048594 aposymbioic hydra M9 strain · aposymbioic hydra rep2 not recorded not recorded aposymbioic hydra rep2 DRP003902 15.60
DRR048595 symbioic hydra M9 strain · symbioic hydra rep1 not recorded not recorded symbioic hydra rep1 DRP003902 10.05
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 correlated0not in this network-
Negatively correlated3g1757-0.543354099769847

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 →
TOP