Detailed information of g19189.t1 in Montipora capitata

Genomic Location: Sc0000989:92076...98263
NR annotation: CAH3110840.1, unnamed protein product [Pocillopora meandrina]
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
Q61025Intraflagellar transport protein 20 homolog OS=Mus musculus OX=10090 GN=Ift20 PE=1 SV=1
Q8IY31Intraflagellar transport protein 20 homolog OS=Homo sapiens OX=9606 GN=IFT20 PE=1 SV=1
Q58CS6Intraflagellar transport protein 20 homolog OS=Bos taurus OX=9913 GN=IFT20 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008484 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF14931
all species →		IFT20Intraflagellar transport complex B, subunit 20FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR028172
all species →		FamilyIntraflagellar transport protein 20Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR31978
all species →		INTRAFLAGELLAR TRANSPORT PROTEIN 20 HOMOLOGInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005794
all species →		Cellular ComponentGolgi apparatusInterproscan
GO:0005813
all species →		Cellular ComponentcentrosomeInterproscan
GO:0005929
all species →		Cellular ComponentciliumInterproscan
GO:0030992
all species →		Cellular Componentintraciliary transport particle BInterproscan
GO:0042073
all species →		Biological Processintraciliary transportInterproscan
GO:0051642
all species →		Biological Processcentrosome localizationInterproscan
GO:0061512
all species →		Biological Processprotein localization to ciliumInterproscan

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
K16473IFT20; intraflagellar transport protein 20-Cilium and associated proteinsko03037deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g19189.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
666.6Max TPM
237.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 231.97 631.71
whole organisms · low pH treatment 15 15 238.67 666.60
whole organisms · extra low pH treatment pH treatment 12 12 246.01 522.98

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 631.71
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 508.97
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 432.15
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 419.62
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 403.40
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 252.64
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 245.17
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 202.22
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 183.43
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 176.30
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 150.21
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 145.30
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 138.40
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 135.30
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 134.73
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 129.42
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 127.39
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 117.42
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 116.36
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 111.91
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 109.24
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 666.60
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 446.52
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 327.90
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 303.24
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 282.21
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 268.87
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 194.94
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 190.22
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 174.31
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 142.79
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 133.57
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 130.04
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 115.36
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 102.74
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 100.80
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 522.98
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 520.07
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 452.91
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 284.34
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 227.53
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 174.57
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 156.87
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 152.81
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 134.10
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 134.03
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 96.88
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 94.96

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 correlated28g20364.t10.970232192708652
Negatively correlated5g15035.t1-0.925909276629411

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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