Detailed information of g10450.t1 in Montipora capitata

Genomic Location: Sc0000292:191460...205061
NR annotation: XP_029192309.1, lissencephaly-1 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
A7S338Lissencephaly-1 homolog OS=Nematostella vectensis OX=45351 GN=v1g242515 PE=3 SV=1
C3XVT5Lissencephaly-1 homolog OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_59218 PE=3 SV=1
Q4RJN5Lissencephaly-1 homolog OS=Tetraodon nigroviridis OX=99883 GN=pafah1b1 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006874 (this species only) · gene tree & orthology
Ubiquitin familyUBD|Other|Beta-prp · all ubiquitin genes in this species
Ubiquitin familyE3|E3 adaptor Cullin RING|CDC20 · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00400
all species →		WD40WD domain, G-beta repeatRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001680
all species →		RepeatWD40 repeatInterproscan
IPR017252
all species →		FamilyDynein regulator LIS1Interproscan
IPR015943
all species →		Homologous_superfamilyWD40/YVTN repeat-like-containing domain superfamilyInterproscan
IPR020472
all species →		RepeatG-protein beta WD-40 repeatInterproscan
IPR036322
all species →		Homologous_superfamilyWD40-repeat-containing domain superfamilyInterproscan
IPR006594
all species →		Conserved_siteLIS1 homology motifInterproscan
IPR037190
all species →		Homologous_superfamilyLIS1, N-terminalInterproscan
IPR019775
all species →		Conserved_siteWD40 repeat, conserved siteInterproscan
IPR050349
all species →		FamilyWD repeat LIS1/nudF dynein regulationInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR44129
all species →		WD REPEAT-CONTAINING PROTEIN POP1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0000132
all species →		Biological Processestablishment of mitotic spindle orientationInterproscan
GO:0000776
all species →		Cellular ComponentkinetochoreInterproscan
GO:0005635
all species →		Cellular Componentnuclear envelopeInterproscan
GO:0005875
all species →		Cellular Componentmicrotubule associated complexInterproscan
GO:0005881
all species →		Cellular Componentcytoplasmic microtubuleInterproscan
GO:0007097
all species →		Biological Processnuclear migrationInterproscan
GO:0031023
all species →		Biological Processmicrotubule organizing center organizationInterproscan
GO:0047496
all species →		Biological Processvesicle transport along microtubuleInterproscan
GO:0051010
all species →		Molecular Functionmicrotubule plus-end bindingInterproscan
GO:0070840
all species →		Molecular Functiondynein complex bindingInterproscan

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
K16794PAFAH1B1, LIS1; platelet-activating factor acetylhydrolase IB subunit alpha-Exosomeko04147deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g10450.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
148.3Max TPM
62.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 68.81 148.31
whole organisms · low pH treatment 15 15 54.66 87.49
whole organisms · extra low pH treatment pH treatment 12 12 59.74 112.10

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 148.31
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 135.29
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 113.65
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 96.29
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 91.03
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 88.91
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 83.37
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 80.71
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 69.72
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 64.91
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 60.56
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 56.68
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 56.19
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 54.24
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 48.03
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 47.63
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 40.77
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 29.62
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 28.44
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 27.76
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 22.88
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 87.49
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 84.93
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 82.54
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 78.90
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 66.29
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 58.76
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 58.36
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 54.90
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 54.73
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 53.48
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 52.98
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 34.40
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 18.81
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 18.51
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 14.90
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 112.10
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 94.77
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 89.10
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 74.55
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 71.98
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 61.12
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 49.40
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 40.01
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 38.94
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 36.19
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 24.68
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 24.05

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 correlated21g4209.t10.958716170678627
Negatively correlated8g2085.t1-0.906468360179054

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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