Detailed information of g3158.t1 in Acropora digitifera

Genomic Location: chr2Alt:9179881...9184647
NR annotation: XP_015750164.1, PREDICTED: transmembrane and coiled-coil domain-containing protein 1-like [Acropora digitifera]
Species Acropora digitifera · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q6DGW9Calcium load-activated calcium channel OS=Danio rerio OX=7955 GN=tmco1 PE=2 SV=1
Q3T0N3Calcium load-activated calcium channel OS=Bos taurus OX=9913 GN=TMCO1 PE=2 SV=1
A0A8I3PI99Calcium load-activated calcium channel OS=Canis lupus familiaris OX=9615 GN=TMCO1 PE=1 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01956
all species →		EMC3_TMCO1Integral membrane protein EMC3/TMCO1-likeFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR008559
all species →		FamilyCalcium load-activated calcium channelInterproscan
IPR002809
all species →		FamilyIntegral membrane protein EMC3/TMCO1-likeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR20917
all species →		PNAS-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005262
all species →		Molecular Functioncalcium channel activityInterproscan
GO:0005789
all species →		Cellular Componentendoplasmic reticulum membraneInterproscan
GO:0032469
all species →		Biological Processendoplasmic reticulum calcium ion homeostasisInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0005783
all species →		Cellular Componentendoplasmic reticulumInterproscan
GO:0006874
all species →		Biological Processintracellular calcium ion homeostasisInterproscan

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
K21891TMCO1; calcium load-activated calcium channel-Transportersko02000deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g3158.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples
39TPM > 0
1Conditions
67.5Max TPM
43.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 43.94 67.47

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 67.47
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 67.14
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 59.68
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 56.22
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 53.83
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 52.87
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 52.47
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 51.32
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 51.30
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 50.45
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 49.87
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 48.02
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 47.00
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 46.79
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 45.84
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 45.52
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 44.00
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 43.83
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 43.55
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 42.61
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 41.22
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 40.80
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 38.60
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 38.49
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 38.09
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 37.52
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 37.46
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 37.34
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 36.84
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 36.46
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 35.90
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 35.66
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 35.44
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 35.42
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 34.99
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 34.75
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 34.04
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 32.57
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 32.19

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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 Acropora digitifera 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 correlated9g23264.t10.823217788508173
Negatively correlated14g16375.t1-0.767547038521189

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 Acropora digitifera, 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.

Peak calls overlapping this gene

AssaySamplePeaksRegion

No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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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