Detailed information of g8582.t1 in Acropora digitifera

Genomic Location: chr4Alt:10564391...10599639
NR annotation: ARA71550.1, cadherin [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
B8V7Q1Protocadherin-like protein OS=Acropora millepora OX=45264 PE=1 SV=1
Q6V0I7Protocadherin Fat 4 OS=Homo sapiens OX=9606 GN=FAT4 PE=1 SV=2
Q2PZL6Protocadherin Fat 4 OS=Mus musculus OX=10090 GN=Fat4 PE=1 SV=2
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02210
all species →		Laminin_G_2Laminin G domainDomainInterproscan
PF01049
all species →		CADH_Y-type_LIRCadherin, Y-type LIR-motifFamilyInterproscan
PF00028
all species →		CadherinCadherin domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001791
all species →		DomainLaminin G domainInterproscan
IPR002126
all species →		DomainCadherin-likeInterproscan
IPR000233
all species →		DomainCadherin, Y-type LIR-motifInterproscan
IPR015919
all species →		Homologous_superfamilyCadherin-like superfamilyInterproscan
IPR000742
all species →		DomainEGF-like domainInterproscan
IPR013320
all species →		Homologous_superfamilyConcanavalin A-like lectin/glucanase domain superfamilyInterproscan
IPR027397
all species →		Homologous_superfamilyCatenin binding domain superfamilyInterproscan
IPR020894
all species →		Conserved_siteCadherin conserved siteInterproscan
IPR039808
all species →		FamilyCadherinInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR24027
all species →		CADHERIN-23Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005509
all species →		Molecular Functioncalcium ion bindingInterproscan
GO:0007156
all species →		Biological Processhomophilic cell adhesion via plasma membrane adhesion moleculesInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0005886
all species →		Cellular Componentplasma membraneInterproscan
GO:0007155
all species →		Biological Processcell adhesionInterproscan
GO:0000902
all species →		Biological Processcell morphogenesisInterproscan
GO:0005912
all species →		Cellular Componentadherens junctionInterproscan
GO:0007043
all species →		Biological Processcell-cell junction assemblyInterproscan
GO:0007275
all species →		Biological Processmulticellular organism developmentInterproscan
GO:0016339
all species →		Biological Processcalcium-dependent cell-cell adhesion via plasma membrane cell adhesion moleculesInterproscan
GO:0016342
all species →		Cellular Componentcatenin complexInterproscan
GO:0034332
all species →		Biological Processadherens junction organizationInterproscan
GO:0044331
all species →		Biological Processcell-cell adhesion mediated by cadherinInterproscan
GO:0045296
all species →		Molecular Functioncadherin bindingInterproscan
GO:0098609
all species →		Biological Processcell-cell adhesionInterproscan
GO:0098742
all species →		Biological Processcell-cell adhesion via plasma-membrane adhesion moleculesInterproscan

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
No KEGG orthology assignment for g8582.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g8582.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
82.4Max TPM
60.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 60.60 82.40

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 82.40
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 77.07
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 75.93
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 75.85
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 75.82
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 73.63
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 73.13
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 72.49
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 71.58
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 70.45
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 67.87
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 67.75
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 66.19
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 65.31
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 64.95
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 64.67
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 63.55
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 63.32
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 61.21
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 60.07
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 59.86
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 59.77
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 58.17
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 58.12
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 56.81
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 56.37
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 53.33
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 53.04
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 52.96
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 52.90
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 52.36
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 52.18
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 49.56
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 48.25
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 46.22
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 45.36
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 44.72
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 42.14
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 28.24

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 correlated31g8524.t10.899329864224021
Negatively correlated8g8385.t1-0.689865082621462

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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