Detailed information of g6553.t1 in Montipora capitata

Genomic Location: Sc0000141:248383...278030
NR annotation: XP_029205518.2, scaffold attachment factor B1-like [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
D3YXK2Scaffold attachment factor B1 OS=Mus musculus OX=10090 GN=Safb PE=1 SV=2
Q14151Scaffold attachment factor B2 OS=Homo sapiens OX=9606 GN=SAFB2 PE=1 SV=1
O88453Scaffold attachment factor B1 OS=Rattus norvegicus OX=10116 GN=Safb PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004754 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00076
all species →		RRM_1RNA recognition motifDomainInterproscan
PF02037
all species →		SAPSAP domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR003034
all species →		DomainSAP domainInterproscan
IPR000504
all species →		DomainRNA recognition motif domainInterproscan
IPR035979
all species →		Homologous_superfamilyRNA-binding domain superfamilyInterproscan
IPR051738
all species →		FamilyScaffold Attachment Factor and ModulatorsInterproscan
IPR012677
all species →		Homologous_superfamilyNucleotide-binding alpha-beta plait domain superfamilyInterproscan
IPR036361
all species →		Homologous_superfamilySAP domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR15683
all species →		SCAFFOLD ATTACHMENT FACTOR B-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0003676
all species →		Molecular Functionnucleic acid bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan
GO:0043565
all species →		Molecular Functionsequence-specific DNA bindingInterproscan
GO:0050684
all species →		Biological Processregulation of mRNA processingInterproscan

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 g6553.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g6553.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
669.2Max TPM
289.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 302.29 663.57
whole organisms · low pH treatment 15 15 301.06 669.22
whole organisms · extra low pH treatment pH treatment 12 12 253.63 618.79

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 663.57
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 613.99
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 610.13
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 601.98
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 533.28
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 474.32
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 462.57
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 448.55
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 297.56
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 204.95
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 183.83
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 176.22
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 175.53
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 175.14
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 139.88
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 138.31
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 98.58
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 94.81
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 94.56
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 90.17
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 70.20
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 669.22
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 647.24
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 606.12
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 588.51
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 515.18
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 418.91
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 152.40
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 138.76
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 135.89
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 133.05
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 131.57
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 117.09
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 100.50
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 93.13
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 68.24
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 618.79
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 569.23
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 455.59
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 384.92
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 170.39
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 169.26
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 164.05
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 146.11
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 144.61
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 90.31
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 73.11
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 57.17

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 correlated37g12499.t10.983013621002927
Negatively correlated16g19456.t1-0.935148212392959

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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