Detailed information of g12051.t1 in Montipora capitata

Genomic Location: Sc0000377:206276...260643
NR annotation: XP_044181966.1, LOW QUALITY PROTEIN: protein scribble homolog [Acropora millepora]
Species Montipora capitata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q4H4B6Protein scribble homolog OS=Danio rerio OX=7955 GN=scrib PE=1 SV=1
A0A8P0N4K0Protein scribble homolog OS=Canis lupus familiaris OX=9615 GN=SCRIB PE=1 SV=1
Q80U72Protein scribble homolog OS=Mus musculus OX=10090 GN=Scrib PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001961 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00595
all species →		PDZPDZ domainDomainInterproscan
PF13855
all species →		LRR_8Leucine rich repeatRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001478
all species →		DomainPDZ domainInterproscan
IPR036034
all species →		Homologous_superfamilyPDZ superfamilyInterproscan
IPR003591
all species →		RepeatLeucine-rich repeat, typical subtypeInterproscan
IPR001611
all species →		RepeatLeucine-rich repeatInterproscan
IPR032675
all species →		Homologous_superfamilyLeucine-rich repeat domain superfamilyInterproscan
IPR050614
all species →		FamilySynaptic Scaffolding LAP/MAGUK FamiliesInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23119
all species →		DISCS LARGEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0005912
all species →		Cellular Componentadherens junctionInterproscan
GO:0009790
all species →		Biological Processembryo developmentInterproscan
GO:0016323
all species →		Cellular Componentbasolateral plasma membraneInterproscan
GO:0030054
all species →		Cellular Componentcell junctionInterproscan
GO:0043113
all species →		Biological Processreceptor clusteringInterproscan
GO:0045197
all species →		Biological Processestablishment or maintenance of epithelial cell apical/basal polarityInterproscan
GO:0097120
all species →		Biological Processreceptor localization to synapseInterproscan
GO:0098609
all species →		Biological Processcell-cell adhesionInterproscan

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
K16175SCRIB; protein scribble-Human papillomavirus infectionko05165deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g12051.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples
48TPM > 0
3Conditions
551.4Max TPM
268.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 243.09 543.89
whole organisms · low pH treatment 15 15 303.98 533.41
whole organisms · extra low pH treatment pH treatment 12 12 266.99 551.39

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 543.89
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 537.29
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 496.09
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 448.82
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 387.61
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 364.33
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 301.78
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 272.81
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 254.96
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 187.59
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 174.95
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 172.93
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 163.40
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 140.77
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 123.33
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 106.21
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 105.56
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 94.85
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 89.30
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 79.88
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 58.64
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 533.41
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 504.48
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 487.68
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 459.37
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 444.60
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 426.29
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 349.98
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 322.31
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 287.61
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 211.75
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 197.22
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 135.26
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 70.01
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 67.48
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 62.20
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 551.39
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 497.13
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 437.11
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 378.27
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 359.09
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 274.26
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 174.12
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 154.77
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 114.88
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 95.70
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 93.45
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 73.72

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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 Montipora capitata 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 correlated35g26628.t10.970704082805001
Negatively correlated26g3499.t1-0.914384957212477

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 Montipora capitata, 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 →
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