Detailed information of agem_s0261.g21.t1 in Acropora gemmifera

Genomic Location: sc0000261_pilon:275616...277894
NR annotation: XP_015763940.1, PREDICTED: lariat debranching enzyme A-like [Acropora digitifera]
Species Acropora gemmifera · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q6GPB8Lariat debranching enzyme A OS=Xenopus laevis OX=8355 GN=dbr1-a PE=2 SV=1
Q5ZLM2Lariat debranching enzyme OS=Gallus gallus OX=9031 GN=DBR1 PE=2 SV=1
Q7T3E4Lariat debranching enzyme OS=Danio rerio OX=7955 GN=dbr1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007864 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00149
all species →		MetallophosCalcineurin-like phosphoesteraseDomainInterproscan
PF05011
all species →		DBR1Lariat debranching enzyme, C-terminal domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR041816
all species →		DomainLariat debranching enzyme, N-terminal metallophosphatase domainInterproscan
IPR007708
all species →		DomainLariat debranching enzyme, C-terminalInterproscan
IPR029052
all species →		Homologous_superfamilyMetallo-dependent phosphatase-likeInterproscan
IPR004843
all species →		DomainCalcineurin-like phosphoesterase domain, ApaH typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12849
all species →		RNA LARIAT DEBRANCHING ENZYMEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006397
all species →		Biological ProcessmRNA processingInterproscan
GO:0016788
all species →		Molecular Functionhydrolase activity, acting on ester bondsInterproscan
GO:0000398
all species →		Biological ProcessmRNA splicing, via spliceosomeInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0008419
all species →		Molecular FunctionRNA lariat debranching enzyme activityInterproscan
GO:0016787
all species →		Molecular Functionhydrolase activityInterproscan

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
K18328DBR1; lariat debranching enzymeEC:3.1.-.-
Ribosome biogenesisko03009deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of agem_s0261.g21.t1 across 48 RNA-seq samples of Acropora gemmifera. 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
29TPM > 0
1Conditions
243.2Max TPM
30.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
branch tip 48 29 29.98 243.20

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR3169540 branch tip branch tip not recorded not recorded SRP062488 243.20
SRR3169541 branch tip branch tip not recorded not recorded SRP062488 222.64
SRR3169421 branch tip branch tip not recorded not recorded SRP062488 204.31
SRR3169538 branch tip branch tip not recorded not recorded SRP062488 100.27
SRR3182792 branch tip branch tip not recorded not recorded SRP062488 77.36
SRR3182794 branch tip branch tip not recorded not recorded SRP062488 61.01
SRR3169423 branch tip branch tip not recorded not recorded SRP062488 51.72
SRR3169535 branch tip branch tip not recorded not recorded SRP062488 49.22
SRR3182686 branch tip branch tip not recorded not recorded SRP062488 45.29
SRR3169530 branch tip branch tip not recorded not recorded SRP062488 36.05
SRR3182789 branch tip branch tip not recorded not recorded SRP062488 33.06
SRR3169426 branch tip branch tip not recorded not recorded SRP062488 32.30
SRR3182775 branch tip branch tip not recorded not recorded SRP062488 32.21
SRR3182684 branch tip branch tip not recorded not recorded SRP062488 28.72
SRR3182787 branch tip branch tip not recorded not recorded SRP062488 26.96
SRR3169532 branch tip branch tip not recorded not recorded SRP062488 22.55
SRR3182781 branch tip branch tip not recorded not recorded SRP062488 21.52
SRR3182410 branch tip branch tip not recorded not recorded SRP062488 18.95
SRR3169539 branch tip branch tip not recorded not recorded SRP062488 18.51
SRR3169425 branch tip branch tip not recorded not recorded SRP062488 17.21
SRR3182776 branch tip branch tip not recorded not recorded SRP062488 15.60
SRR2169558 branch tip branch tip not recorded not recorded SRP062488 14.96
SRR3169531 branch tip branch tip not recorded not recorded SRP062488 14.83
SRR3223317 branch tip branch tip not recorded not recorded SRP062488 13.81
SRR3182785 branch tip branch tip not recorded not recorded SRP062488 9.21
SRR3169518 branch tip branch tip not recorded not recorded SRP062488 8.99
SRR3223319 branch tip branch tip not recorded not recorded SRP062488 7.66
SRR3169528 branch tip branch tip not recorded not recorded SRP062488 6.26
SRR3182788 branch tip branch tip not recorded not recorded SRP062488 4.68
SRR3169422 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169527 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169529 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169533 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169534 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169536 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169537 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182448 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182557 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182685 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182777 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182778 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182779 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182780 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182784 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182786 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182790 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182791 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182793 branch tip branch tip not recorded not recorded SRP062488 0.00

Source: CnidoSite RNA-seq expression matrices (AGEMM_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 Acropora gemmifera 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 correlated16agem_s0104.g92.t1-0.374673441857787

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 gemmifera, 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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