Detailed information of XP_074630404.1 in Acropora palmata

Genomic Location: NC_133889.1:8041530...8054811
NR annotation: XP_029201893.2, transcription factor IIIB 90 kDa subunit-like isoform X3 [Acropora millepora]
Species Acropora palmata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q92994Transcription factor IIIB 90 kDa subunit OS=Homo sapiens OX=9606 GN=BRF1 PE=1 SV=1
Q8CFK2Transcription factor IIIB 90 kDa subunit OS=Mus musculus OX=10090 GN=Brf1 PE=1 SV=1
Q9P6R0Transcription factor IIIB 60 kDa subunit OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=brf1 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003241 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00382
all species →		TFIIBTranscription factor TFIIB repeatDomainInterproscan
PF07741
all species →		BRF1Brf1-like TBP-binding domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR013763
all species →		DomainCyclin-like domainInterproscan
IPR013150
all species →		DomainTranscription factor TFIIB, cyclin-like domainInterproscan
IPR036915
all species →		Homologous_superfamilyCyclin-like superfamilyInterproscan
IPR011665
all species →		DomainBrf1, TBP-binding domainInterproscan
IPR000812
all species →		FamilyTranscription factor TFIIBInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11618
all species →		TRANSCRIPTION INITIATION FACTOR IIB-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0017025
all species →		Molecular FunctionTBP-class protein bindingInterproscan
GO:0000126
all species →		Cellular Componenttranscription factor TFIIIB complexInterproscan
GO:0000995
all species →		Molecular FunctionRNA polymerase III general transcription initiation factor activityInterproscan
GO:0001006
all species →		Molecular FunctionRNA polymerase III type 3 promoter sequence-specific DNA bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006352
all species →		Biological ProcessDNA-templated transcription initiationInterproscan
GO:0006383
all species →		Biological Processtranscription by RNA polymerase IIIInterproscan
GO:0070897
all species →		Biological Processtranscription preinitiation complex assemblyInterproscan
GO:0097550
all species →		Cellular Componenttranscription preinitiation complexInterproscan

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
K15196BRF1, GTF3B; transcription factor IIIB 90 kDa subunit-Transcription machineryko03021deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_074630404.1 across 84 RNA-seq samples of Acropora palmata. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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.

84Samples
0TPM > 0
2Conditions
0.0Max TPM
0.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
all_coral_tissue · exposed 46 0 0.00 0.00
all_coral_tissue · baseline 38 0 0.00 0.00

Per sample · hover a bar for the full sample record

Show the sample table (84 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR8800026 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800027 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800028 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800029 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800033 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800034 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800036 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800038 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800039 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800040 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800042 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800044 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800045 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800047 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800051 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800053 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800056 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800058 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800060 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800061 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800062 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800063 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800065 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800066 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800068 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800071 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800073 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800075 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800077 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800079 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800080 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800083 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800086 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800087 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800088 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800089 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800091 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800092 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800093 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800094 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800095 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800097 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800099 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800100 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800105 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800107 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800030 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800031 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800032 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800035 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800037 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800041 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800043 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800046 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800048 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800049 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800050 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800052 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800054 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800055 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800057 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800059 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800064 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800067 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800069 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800070 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800072 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800074 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800076 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800078 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800081 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800082 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800084 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800085 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800090 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800096 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800098 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800101 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800102 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800103 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800104 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800106 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800108 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800109 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00

Source: CnidoSite RNA-seq expression matrices (APALM_TPM, StringTie quantification over 84 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 Acropora palmata 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 correlated0not in this network-
Negatively correlated0not in this network-

This gene has no edge at all in the Acropora palmata network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.

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 Acropora palmata, 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.

DNA methylation (bisulphite samples)

SampleMethylation profile
Polyp_Underside_Control_2open
Polyp_Underside_Control_3open
Polyp_Underside_Treatment_1open
Polyp_Upperside_Control_1open
Polyp_Upperside_Treatment_3open
Polyp_Upperside_Treatment_4open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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.no expression matrix–
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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