Detailed information of asel_s0409.g3.t1 in Acropora selago

Genomic Location: sc0000409_pilon:68816...69948
NR annotation: XP_029208961.1, protein lyl-1-like [Acropora millepora]
Species Acropora selago · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P27792Protein lyl-1 OS=Mus musculus OX=10090 GN=Lyl1 PE=2 SV=2
Q66HH3Protein lyl-1 OS=Rattus norvegicus OX=10116 GN=Lyl1 PE=2 SV=1
P12980Protein lyl-1 OS=Homo sapiens OX=9606 GN=LYL1 PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000221 (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
IPR011598
all species →		DomainMyc-type, basic helix-loop-helix (bHLH) domainInterproscan
IPR036638
all species →		Homologous_superfamilyHelix-loop-helix DNA-binding domain superfamilyInterproscan
IPR040238
all species →		FamilyHelix-loop-helix protein TAL-likeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13864
all species →		T-CELL ACUTE LYMPHOCYTIC LEUKEMIA/STEM CELL LEUKEMIA-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0046983
all species →		Molecular Functionprotein dimerization activityInterproscan
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: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
K09068TAL; T-cell acute lymphocytic leukemia protein-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 asel_s0409.g3.t1 across 24 RNA-seq samples of Acropora selago. 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.

24Samples
23TPM > 0
1Conditions
72.9Max TPM
12.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
coral larvae 24 23 12.58 72.89

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR14308024 coral larvae coral larvae not recorded not recorded SRP315987 72.89
SRR14308011 coral larvae coral larvae not recorded not recorded SRP315987 49.63
SRR14308018 coral larvae coral larvae not recorded not recorded SRP315987 40.45
SRR14308019 coral larvae coral larvae not recorded not recorded SRP315987 28.28
SRR14308009 coral larvae coral larvae not recorded not recorded SRP315987 24.78
SRR14308012 coral larvae coral larvae not recorded not recorded SRP315987 23.47
SRR14308008 coral larvae coral larvae not recorded not recorded SRP315987 11.64
SRR14308025 coral larvae coral larvae not recorded not recorded SRP315987 7.58
SRR14308006 coral larvae coral larvae not recorded not recorded SRP315987 7.23
SRR14308026 coral larvae coral larvae not recorded not recorded SRP315987 5.49
SRR14308022 coral larvae coral larvae not recorded not recorded SRP315987 5.00
SRR14308020 coral larvae coral larvae not recorded not recorded SRP315987 4.82
SRR14308021 coral larvae coral larvae not recorded not recorded SRP315987 3.63
SRR14308013 coral larvae coral larvae not recorded not recorded SRP315987 2.94
SRR14308014 coral larvae coral larvae not recorded not recorded SRP315987 2.86
SRR14308016 coral larvae coral larvae not recorded not recorded SRP315987 2.30
SRR14308010 coral larvae coral larvae not recorded not recorded SRP315987 1.65
SRR14308017 coral larvae coral larvae not recorded not recorded SRP315987 1.65
SRR14308015 coral larvae coral larvae not recorded not recorded SRP315987 1.63
SRR14308027 coral larvae coral larvae not recorded not recorded SRP315987 1.45
SRR14308004 coral larvae coral larvae not recorded not recorded SRP315987 1.11
SRR14308023 coral larvae coral larvae not recorded not recorded SRP315987 1.02
SRR14308007 coral larvae coral larvae not recorded not recorded SRP315987 0.53
SRR14308005 coral larvae coral larvae not recorded not recorded SRP315987 0.00

Source: CnidoSite RNA-seq expression matrices (ASELA_TPM, StringTie quantification over 24 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 selago 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 correlated38asel_s0168.g44.t10.955859556839704
Negatively correlated30asel_s0343.g17.t1-0.858427217176145

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 selago, 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
Coral_Fragment_Parentopen
Larval_Pool_Offspringopen

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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