Detailed information of agem_s0126.g13.t1 in Acropora gemmifera

Genomic Location: sc0000126_pilon:138926...154895
NR annotation: XP_044184184.1, LARGE xylosyl- and glucuronyltransferase 2-like [Acropora millepora]
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
Q9Z1M7Xylosyl- and glucuronyltransferase LARGE1 OS=Mus musculus OX=10090 GN=Large1 PE=1 SV=1
Q66PG1Xylosyl- and glucuronyltransferase LARGE2s OS=Danio rerio OX=7955 GN=large2 PE=2 SV=1
O95461Xylosyl- and glucuronyltransferase LARGE1 OS=Homo sapiens OX=9606 GN=LARGE1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003897 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13896
all species →		Glyco_transf_49Glycosyl-transferase for dystroglycanDomainInterproscan
PF01501
all species →		Glyco_transf_8Glycosyl transferase family 8FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR029044
all species →		Homologous_superfamilyNucleotide-diphospho-sugar transferasesInterproscan
IPR051292
all species →		FamilyAlpha-1,3-xylosyltransferase/Beta-1,3-glucuronyltransferaseInterproscan
IPR002495
all species →		FamilyGlycosyl transferase, family 8Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12270
all species →		GLYCOSYLTRANSFERASE-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0015020
all species →		Molecular Functionglucuronosyltransferase activityInterproscan
GO:0035269
all species →		Biological Processprotein O-linked mannosylationInterproscan
GO:0042285
all species →		Molecular Functionxylosyltransferase activityInterproscan
GO:0016757
all species →		Molecular Functionglycosyltransferase 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
K09668LARGE; glycosyltransferase-like protein LARGEEC:2.4.2.-
EC:2.4.1.-
Glycosyltransferasesko01003deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of agem_s0126.g13.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
32TPM > 0
1Conditions
557.7Max TPM
167.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
branch tip 48 32 167.30 557.74

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR3169529 branch tip branch tip not recorded not recorded SRP062488 557.74
SRR3169541 branch tip branch tip not recorded not recorded SRP062488 552.07
SRR3169530 branch tip branch tip not recorded not recorded SRP062488 392.20
SRR3182790 branch tip branch tip not recorded not recorded SRP062488 370.32
SRR3182778 branch tip branch tip not recorded not recorded SRP062488 368.02
SRR3169538 branch tip branch tip not recorded not recorded SRP062488 364.43
SRR3169535 branch tip branch tip not recorded not recorded SRP062488 351.41
SRR3169539 branch tip branch tip not recorded not recorded SRP062488 347.66
SRR3169518 branch tip branch tip not recorded not recorded SRP062488 339.38
SRR3169531 branch tip branch tip not recorded not recorded SRP062488 332.48
SRR3169425 branch tip branch tip not recorded not recorded SRP062488 327.82
SRR3169528 branch tip branch tip not recorded not recorded SRP062488 306.54
SRR3169423 branch tip branch tip not recorded not recorded SRP062488 303.00
SRR3182448 branch tip branch tip not recorded not recorded SRP062488 296.74
SRR3182785 branch tip branch tip not recorded not recorded SRP062488 284.19
SRR3182793 branch tip branch tip not recorded not recorded SRP062488 283.30
SRR3169532 branch tip branch tip not recorded not recorded SRP062488 267.73
SRR3169422 branch tip branch tip not recorded not recorded SRP062488 243.30
SRR3169537 branch tip branch tip not recorded not recorded SRP062488 209.80
SRR3182775 branch tip branch tip not recorded not recorded SRP062488 202.79
SRR3169527 branch tip branch tip not recorded not recorded SRP062488 196.78
SRR3169540 branch tip branch tip not recorded not recorded SRP062488 169.08
SRR3182686 branch tip branch tip not recorded not recorded SRP062488 160.20
SRR3169426 branch tip branch tip not recorded not recorded SRP062488 153.18
SRR3182410 branch tip branch tip not recorded not recorded SRP062488 139.53
SRR3182787 branch tip branch tip not recorded not recorded SRP062488 136.12
SRR3182792 branch tip branch tip not recorded not recorded SRP062488 133.28
SRR3182794 branch tip branch tip not recorded not recorded SRP062488 104.53
SRR3182784 branch tip branch tip not recorded not recorded SRP062488 82.41
SRR3223317 branch tip branch tip not recorded not recorded SRP062488 21.62
SRR2169558 branch tip branch tip not recorded not recorded SRP062488 18.75
SRR3223319 branch tip branch tip not recorded not recorded SRP062488 13.91
SRR3169421 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
SRR3182557 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182684 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182685 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182776 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182777 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
SRR3182781 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182786 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182788 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182789 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182791 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 correlated36agem_s0193.g39.t1-0.367786179678768

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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