Detailed information of KXJ27168.1 in Exaiptasia diaphana

Genomic Location: LJWW01000023.1:801227...826358
NR annotation: KXJ27168.1, Transcription factor 12 [Exaiptasia diaphana]
Species Exaiptasia diaphana · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q61286Transcription factor 12 OS=Mus musculus OX=10090 GN=Tcf12 PE=1 SV=2
Q99081Transcription factor 12 OS=Homo sapiens OX=9606 GN=TCF12 PE=1 SV=1
P51514Transcription factor 12 OS=Rattus norvegicus OX=10116 GN=Tcf12 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001322 (this species only) · gene tree & orthology
Transcription factor familybHLH · all TF in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00010
all species →		HLHHelix-loop-helix DNA-binding domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036638
all species →		Homologous_superfamilyHelix-loop-helix DNA-binding domain superfamilyInterproscan
IPR011598
all species →		DomainMyc-type, basic helix-loop-helix (bHLH) domainInterproscan
IPR051098
all species →		FamilyNeuronal Differentiation E-box Binding Transcription FactorsInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11793
all species →		BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0046983
all species →		Molecular Functionprotein dimerization activityInterproscan
GO:0000790
all species →		Cellular ComponentchromatinInterproscan
GO:0000978
all species →		Molecular FunctionRNA polymerase II cis-regulatory region sequence-specific DNA bindingInterproscan
GO:0000981
all species →		Molecular FunctionDNA-binding transcription factor activity, RNA polymerase II-specificInterproscan
GO:0005667
all species →		Cellular Componenttranscription regulator complexInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan

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
K15603TCF4_12; transcription factor 4/12-Transcription factorsko03000deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of KXJ27168.1 across 72 RNA-seq samples of Exaiptasia diaphana. 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.

72Samples
70TPM > 0
2Conditions
161.2Max TPM
81.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole animal · aposymbiotic 36 34 59.69 129.95
whole animal · symbiotic 36 36 102.28 161.17

Per sample · hover a bar for the full sample record

Show the sample table (72 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR6202345 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 129.95
SRR6202233 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 86.90
SRR6202260 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 83.65
SRR6202234 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 83.45
SRR6202241 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 82.06
SRR6202261 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 80.37
SRR6202258 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 79.93
SRR6202242 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 79.40
SRR6202259 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 79.20
SRR6202346 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 77.35
SRR6202210 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 77.19
SRR6202212 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 76.93
SRR6202211 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 74.79
SRR6202209 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 71.02
SRR6202358 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 70.29
SRR6202344 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 68.54
SRR6202206 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 61.99
SRR6202208 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 61.68
SRR6202207 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 59.44
SRR6202363 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 57.80
SRR6202205 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 54.88
SRR6202255 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 53.55
SRR6202238 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 52.90
SRR6202254 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 49.75
SRR6202343 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 49.41
SRR6202235 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 48.90
SRR6202237 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 47.42
SRR6202236 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 45.45
SRR6202204 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 37.43
SRR6202240 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 35.34
SRR6202256 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 34.24
SRR6202203 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 33.54
SRR6202239 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 32.74
SRR6202257 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 31.40
SRR6202357 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202364 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202342 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 161.17
SRR6202353 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 151.74
SRR6202285 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 132.13
SRR6202305 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 130.47
SRR6202282 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 127.57
SRR6202306 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 127.06
SRR6202304 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 126.46
SRR6202303 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 126.02
SRR6202284 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 124.53
SRR6202283 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 123.85
SRR6202309 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 118.31
SRR6202308 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 117.67
SRR6202307 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 117.33
SRR6202262 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 116.47
SRR6202310 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 116.26
SRR6202340 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 109.61
SRR6202263 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 109.05
SRR6202339 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 107.98
SRR6202341 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 107.70
SRR6202349 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 94.59
SRR6202354 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 87.90
SRR6202337 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 84.27
SRR6202276 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 81.96
SRR6202350 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 80.40
SRR6202338 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 79.96
SRR6202279 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 79.75
SRR6202277 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 79.12
SRR6202355 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 78.81
SRR6202356 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 77.55
SRR6202278 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 76.92
SRR6202347 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 76.27
SRR6202348 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 72.13
SRR6202351 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 71.92
SRR6202281 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 70.92
SRR6202280 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 69.53
SRR6202352 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 68.80

Source: CnidoSite RNA-seq expression matrices (EDIAP_TPM, StringTie quantification over 72 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 Exaiptasia diaphana 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 correlated31KXJ25963.10.923668647694176
Negatively correlated11KXJ24381.1-0.837738783356979

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 Exaiptasia diaphana, 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.

Peak calls overlapping this gene

AssaySamplePeaksRegion
ChIP-seqH3K27ac_symbiont2Promoter (1-2kb) 1 · Promoter (<=1kb) 1
H3K9ac_symbiont5Intron 3 · Promoter (<=1kb) 2
ATAC-seqMild_Stress_Aposym1Promoter (<=1kb) 1

Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.

DNA methylation (bisulphite samples)

SampleMethylation profile
whole_animal_aposymbiotic_1open
whole_animal_aposymbiotic_2open
whole_animal_aposymbiotic_3open
whole_animal_aposymbiotic_4open
whole_animal_aposymbiotic_5open
whole_animal_aposymbiotic_6open
whole_animal_aposymbiotic_7open
whole_animal_aposymbiotic_8open
whole_animal_aposymbiotic_9open
whole_animal_symbiotic_1open
whole_animal_symbiotic_10open
whole_animal_symbiotic_11open
whole_animal_symbiotic_12open
whole_animal_symbiotic_13open
whole_animal_symbiotic_14open
whole_animal_symbiotic_2open
whole_animal_symbiotic_3open
whole_animal_symbiotic_4open
whole_animal_symbiotic_5open
whole_animal_symbiotic_6open
whole_animal_symbiotic_7open
whole_animal_symbiotic_8open
whole_animal_symbiotic_9open

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.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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