Detailed information of g6614.t1 in Montipora capitata

Genomic Location: Sc0000143:157792...204689
NR annotation: XP_015777077.1, PREDICTED: collagen alpha-1(IX) chain-like isoform X1 [Acropora digitifera]
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
P13942Collagen alpha-2(XI) chain OS=Homo sapiens OX=9606 GN=COL11A2 PE=1 SV=5
Q64739Collagen alpha-2(XI) chain OS=Mus musculus OX=10090 GN=Col11a2 PE=2 SV=3
Q32S24Collagen alpha-2(XI) chain OS=Bos taurus OX=9913 GN=COL11A2 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000267 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01391
all species →		CollagenCollagen triple helix repeat (20 copies)RepeatInterproscan
PF02210
all species →		Laminin_G_2Laminin G domainDomainInterproscan
PF01410
all species →		COLFIFibrillar collagen C-terminal domainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR008160
all species →		RepeatCollagen triple helix repeatInterproscan
IPR013320
all species →		Homologous_superfamilyConcanavalin A-like lectin/glucanase domain superfamilyInterproscan
IPR001791
all species →		DomainLaminin G domainInterproscan
IPR048287
all species →		DomainThrombospondin-like, N-terminal domainInterproscan
IPR000885
all species →		DomainFibrillar collagen, C-terminalInterproscan
IPR050149
all species →		FamilyCollagen superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR24023
all species →		COLLAGEN ALPHAInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005201
all species →		Molecular Functionextracellular matrix structural constituentInterproscan
GO:0005615
all species →		Cellular Componentextracellular spaceInterproscan
GO:0030020
all species →		Molecular Functionextracellular matrix structural constituent conferring tensile strengthInterproscan
GO:0030198
all species →		Biological Processextracellular matrix organizationInterproscan
GO:0031012
all species →		Cellular Componentextracellular matrixInterproscan
GO:0062023
all species →		Cellular Componentcollagen-containing extracellular matrixInterproscan

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 g6614.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g6614.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
18TPM > 0
3Conditions
158.5Max TPM
22.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 9 21.33 158.52
whole organisms · low pH treatment 15 4 18.67 102.85
whole organisms · extra low pH treatment pH treatment 12 5 28.70 136.45

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 158.52
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 112.74
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 102.76
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 38.49
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 19.35
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 8.92
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 6.30
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 0.56
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 0.24
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 0.00
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 0.00
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 0.00
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 0.00
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 0.00
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 0.00
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 0.00
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 0.00
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 0.00
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 0.00
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 0.00
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 0.00
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 102.85
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 96.91
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 79.27
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 0.97
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 0.00
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 0.00
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 0.00
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 0.00
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 0.00
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 0.00
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 0.00
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 0.00
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 0.00
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 0.00
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 0.00
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 136.45
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 126.06
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 80.46
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 0.76
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 0.68
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 0.00
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 0.00
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 0.00
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 0.00
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 0.00
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 0.00
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 0.00

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 correlated41g17806.t10.99698600345586
Negatively correlated3g6649.t1-0.894800353356545

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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