Detailed information of g29947.t1 in Acropora digitifera

Genomic Location: chr14Alt:10828311...10839582
NR annotation: XP_029203614.2, cathepsin B-like CP3 [Acropora millepora]
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
Q94K85Cathepsin B-like protease 3 OS=Arabidopsis thaliana OX=3702 GN=CATHB3 PE=1 SV=1
Q93VC9Cathepsin B-like protease 2 OS=Arabidopsis thaliana OX=3702 GN=CATHB2 PE=2 SV=1
P43508Cathepsin B-like cysteine proteinase 4 OS=Caenorhabditis elegans OX=6239 GN=cpr-4 PE=1 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00112
all species →		Peptidase_C1Papain family cysteine proteaseDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR025660
all species →		Active_siteCysteine peptidase, histidine active siteInterproscan
IPR038765
all species →		Homologous_superfamilyPapain-like cysteine peptidase superfamilyInterproscan
IPR025661
all species →		Active_siteCysteine peptidase, asparagine active siteInterproscan
IPR000169
all species →		Active_siteCysteine peptidase, cysteine active siteInterproscan
IPR013128
all species →		FamilyPeptidase C1AInterproscan
IPR000668
all species →		DomainPeptidase C1A, papain C-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12411
all species →		CYSTEINE PROTEASE FAMILY C1-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004197
all species →		Molecular Functioncysteine-type endopeptidase activityInterproscan
GO:0005615
all species →		Cellular Componentextracellular spaceInterproscan
GO:0005764
all species →		Cellular ComponentlysosomeInterproscan
GO:0008234
all species →		Molecular Functioncysteine-type peptidase activityInterproscan
GO:0051603
all species →		Biological Processproteolysis involved in protein catabolic processInterproscan
GO:0006508
all species →		Biological ProcessproteolysisInterproscan

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 g29947.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g29947.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
505.5Max TPM
358.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 358.26 505.50

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 505.50
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 489.71
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 481.88
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 480.09
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 469.71
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 461.37
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 456.84
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 442.20
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 437.25
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 425.38
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 419.31
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 416.35
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 407.29
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 404.75
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 401.98
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 391.06
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 390.40
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 385.86
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 367.21
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 365.45
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 352.69
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 351.97
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 349.55
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 342.04
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 338.50
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 332.36
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 332.04
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 322.39
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 297.48
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 289.11
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 275.59
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 272.44
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 266.40
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 257.46
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 252.30
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 236.65
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 203.67
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 174.66
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 125.36

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 correlated12g19397.t10.777020402631692
Negatively correlated44g21506.t1-0.830591289440897

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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