Detailed information of KXJ08212.1 in Exaiptasia diaphana

Genomic Location: LJWW01000581.1:72896...84515
NR annotation: XP_020911359.1, visual system homeobox 2 [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
P58304Visual system homeobox 2 OS=Homo sapiens OX=9606 GN=VSX2 PE=1 SV=1
Q61412Visual system homeobox 2 OS=Mus musculus OX=10090 GN=Vsx2 PE=1 SV=1
Q9IAL1Visual system homeobox 2 OS=Gallus gallus OX=9031 GN=VSX2 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000263 (this species only) · gene tree & orthology
Transcription factor familyHomeobox · all TF in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00046
all species →		HomeodomainHomeodomainDomainInterproscan
PF03826
all species →		OAROAR motifMotifInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001356
all species →		DomainHomeobox domainInterproscan
IPR003654
all species →		DomainOAR domainInterproscan
IPR009057
all species →		Homologous_superfamilyHomeobox-like domain superfamilyInterproscan
IPR052294
all species →		FamilyVisual system homeobox transcriptional regulatorsInterproscan
IPR017970
all species →		Conserved_siteHomeobox, conserved siteInterproscan
IPR023339
all species →		DomainCVC domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR46892
all species →		VISUAL SYSTEM HOMEOBOX 2Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan
GO:1990837
all species →		Molecular Functionsequence-specific double-stranded DNA bindingInterproscan
GO:0000981
all species →		Molecular FunctionDNA-binding transcription factor activity, RNA polymerase II-specificInterproscan
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan

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
K09335VSX1; visual system homeobox protein 1-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 KXJ08212.1 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
60TPM > 0
2Conditions
10.2Max TPM
3.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole animal · aposymbiotic 36 29 3.11 8.22
whole animal · symbiotic 36 31 4.52 10.22

Per sample · hover a bar for the full sample record

Show the sample table (72 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR6202241 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 8.22
SRR6202358 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 7.25
SRR6202261 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 5.91
SRR6202242 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 5.64
SRR6202235 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 5.31
SRR6202260 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 5.20
SRR6202259 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 5.14
SRR6202346 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 4.97
SRR6202209 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 4.69
SRR6202206 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 4.69
SRR6202211 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 4.31
SRR6202258 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 4.17
SRR6202205 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.98
SRR6202212 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.66
SRR6202210 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.65
SRR6202236 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.63
SRR6202234 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.59
SRR6202254 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.29
SRR6202255 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.24
SRR6202208 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.23
SRR6202233 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 3.00
SRR6202238 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 2.67
SRR6202256 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 2.55
SRR6202203 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 2.10
SRR6202237 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 1.92
SRR6202239 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 1.81
SRR6202257 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 1.49
SRR6202204 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 1.33
SRR6202207 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 1.23
SRR6202240 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202343 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202344 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202345 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202357 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202363 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202364 whole animal · aposymbiotic whole animal not recorded aposymbiotic SRP120942 0.00
SRR6202356 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 10.22
SRR6202303 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 9.78
SRR6202305 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 7.81
SRR6202304 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 7.76
SRR6202281 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 6.38
SRR6202309 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 6.30
SRR6202279 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 6.22
SRR6202308 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 6.08
SRR6202340 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 6.00
SRR6202262 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 5.73
SRR6202282 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 5.72
SRR6202284 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 5.65
SRR6202306 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 5.28
SRR6202285 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 5.17
SRR6202263 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 5.07
SRR6202277 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.98
SRR6202351 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.93
SRR6202338 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.92
SRR6202307 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.44
SRR6202339 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.42
SRR6202341 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.35
SRR6202355 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.20
SRR6202276 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.18
SRR6202278 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 4.09
SRR6202283 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 3.99
SRR6202352 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 3.70
SRR6202310 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 3.66
SRR6202280 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 3.54
SRR6202337 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 3.31
SRR6202347 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 3.19
SRR6202350 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 1.82
SRR6202342 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 0.00
SRR6202348 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 0.00
SRR6202349 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 0.00
SRR6202353 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 0.00
SRR6202354 whole animal · symbiotic whole animal not recorded symbiotic SRP120942 0.00

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 correlated12KXJ14301.10.81560304909752
Negatively correlated3KXJ19505.1-0.642873293396769

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

No called peak overlaps this gene in 2 available assays. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

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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