Detailed information of g2196.t1 in Acropora digitifera

Genomic Location: chr1Alt:35473539...35487457
NR annotation: XP_029190421.2, A disintegrin and metalloproteinase with thrombospondin motifs 6-like isoform X3 [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
Q9UKP5A disintegrin and metalloproteinase with thrombospondin motifs 6 OS=Homo sapiens OX=9606 GN=ADAMTS6 PE=1 SV=2
Q8TE60A disintegrin and metalloproteinase with thrombospondin motifs 18 OS=Homo sapiens OX=9606 GN=ADAMTS18 PE=1 SV=3
Q811B3A disintegrin and metalloproteinase with thrombospondin motifs 12 OS=Mus musculus OX=10090 GN=Adamts12 PE=2 SV=2
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01421
all species →		ReprolysinReprolysin (M12B) family zinc metalloprotease DomainInterproscan
PF05986
all species →		ADAMTS_spacer1ADAM-TS Spacer 1DomainInterproscan
PF17771
all species →		ADAMTS_CR_2ADAMTS cysteine-rich domain 2DomainInterproscan
PF00090
all species →		TSP_1Thrombospondin type 1 domainDomainInterproscan
PF01562
all species →		Pep_M12B_propepReprolysin family propeptideFamilyInterproscan
PF19236
all species →		ADAMTS_CR_3ADAMTS cysteine-rich domainDomainInterproscan
PF19030
all species →		TSP1_ADAMTSThrombospondin type 1 domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001590
all species →		DomainPeptidase M12B, ADAM/reprolysinInterproscan
IPR036383
all species →		Homologous_superfamilyThrombospondin type-1 (TSP1) repeat superfamilyInterproscan
IPR000884
all species →		RepeatThrombospondin type-1 (TSP1) repeatInterproscan
IPR050439
all species →		FamilyADAMTS and ADAMTS-likeInterproscan
IPR010294
all species →		DomainADAMTS/ADAMTS-like, Spacer 1Interproscan
IPR024079
all species →		Homologous_superfamilyMetallopeptidase, catalytic domain superfamilyInterproscan
IPR041645
all species →		DomainADAMTS, cysteine-rich domain 2Interproscan
IPR013273
all species →		FamilyADAMTS/ADAMTS-likeInterproscan
IPR002870
all species →		DomainPeptidase M12B, propeptideInterproscan
IPR006586
all species →		DomainADAM, cysteine-rich domainInterproscan
IPR045371
all species →		DomainADAMTS/ADAMTS-like, cysteine-rich domain 3Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13723
all species →		ADAMTS A DISINTEGRIN AND METALLOPROTEASE WITH THROMBOSPONDIN MOTIFS PROTEASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004222
all species →		Molecular Functionmetalloendopeptidase activityInterproscan
GO:0006508
all species →		Biological ProcessproteolysisInterproscan
GO:0030198
all species →		Biological Processextracellular matrix organizationInterproscan
GO:0031012
all species →		Cellular Componentextracellular matrixInterproscan
GO:0008237
all species →		Molecular Functionmetallopeptidase activityInterproscan

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 g2196.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g2196.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
55.7Max TPM
29.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 29.11 55.74

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 55.74
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 51.03
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 46.34
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 46.11
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 45.61
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 42.13
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 42.12
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 41.26
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 40.07
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 38.73
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 38.46
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 35.26
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 34.84
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 34.73
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 32.67
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 31.97
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 29.29
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 27.76
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 26.99
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 26.24
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 26.04
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 25.34
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 23.83
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 23.23
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 21.89
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 21.49
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 21.25
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 20.68
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 20.03
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 19.68
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 18.92
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 18.84
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 18.41
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 18.35
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 16.02
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 14.98
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 14.57
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 13.85
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 10.37

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 correlated16g10386.t10.810508961465974
Negatively correlated13g11592.t1-0.775476415210178

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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