Detailed information of agem_s0325.g17.t1 in Acropora gemmifera

Genomic Location: sc0000325_pilon:246636...266240
NR annotation: XP_029204963.2, leucine-rich repeat and coiled-coil domain-containing protein 1-like isoform X2 [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
Q6NRC9Leucine-rich repeat and coiled-coil domain-containing protein 1 OS=Xenopus laevis OX=8355 GN=lrrcc1 PE=2 SV=1
Q69ZB0Leucine-rich repeat and coiled-coil domain-containing protein 1 OS=Mus musculus OX=10090 GN=Lrrcc1 PE=2 SV=2
Q9C099Leucine-rich repeat and coiled-coil domain-containing protein 1 OS=Homo sapiens OX=9606 GN=LRRCC1 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003798 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF12799
all species →		LRR_4Leucine Rich repeats (2 copies)RepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR025875
all species →		RepeatLeucine rich repeat 4Interproscan
IPR001611
all species →		RepeatLeucine-rich repeatInterproscan
IPR032675
all species →		Homologous_superfamilyLeucine-rich repeat domain superfamilyInterproscan
IPR050576
all species →		FamilyCiliary and flagellar integrity-associated proteinInterproscan
IPR003591
all species →		RepeatLeucine-rich repeat, typical subtypeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45973
all species →		PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT SDS22-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan

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
K16475LRRCC1, CLERC; leucine-rich repeat and coiled-coil domain-containing protein 1-Chromosome and associated proteinsko03036deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of agem_s0325.g17.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
5,363.1Max TPM
372.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
branch tip 48 29 372.54 5,363.15

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR3182777 branch tip branch tip not recorded not recorded SRP062488 5,363.15
SRR3182778 branch tip branch tip not recorded not recorded SRP062488 1,434.17
SRR3182784 branch tip branch tip not recorded not recorded SRP062488 1,020.45
SRR3182780 branch tip branch tip not recorded not recorded SRP062488 788.44
SRR3169529 branch tip branch tip not recorded not recorded SRP062488 776.83
SRR3182785 branch tip branch tip not recorded not recorded SRP062488 740.72
SRR3182790 branch tip branch tip not recorded not recorded SRP062488 710.80
SRR3182779 branch tip branch tip not recorded not recorded SRP062488 685.03
SRR3169531 branch tip branch tip not recorded not recorded SRP062488 664.66
SRR3169530 branch tip branch tip not recorded not recorded SRP062488 595.38
SRR3169532 branch tip branch tip not recorded not recorded SRP062488 519.56
SRR3182775 branch tip branch tip not recorded not recorded SRP062488 464.77
SRR3169425 branch tip branch tip not recorded not recorded SRP062488 452.20
SRR3182793 branch tip branch tip not recorded not recorded SRP062488 437.65
SRR3182787 branch tip branch tip not recorded not recorded SRP062488 396.27
SRR3182794 branch tip branch tip not recorded not recorded SRP062488 372.82
SRR3169534 branch tip branch tip not recorded not recorded SRP062488 361.04
SRR3182686 branch tip branch tip not recorded not recorded SRP062488 326.19
SRR3169426 branch tip branch tip not recorded not recorded SRP062488 323.74
SRR3182792 branch tip branch tip not recorded not recorded SRP062488 310.45
SRR3169422 branch tip branch tip not recorded not recorded SRP062488 307.75
SRR3169527 branch tip branch tip not recorded not recorded SRP062488 304.54
SRR3182789 branch tip branch tip not recorded not recorded SRP062488 242.94
SRR3169423 branch tip branch tip not recorded not recorded SRP062488 148.88
SRR3182788 branch tip branch tip not recorded not recorded SRP062488 43.01
SRR3182791 branch tip branch tip not recorded not recorded SRP062488 31.99
SRR3223319 branch tip branch tip not recorded not recorded SRP062488 25.55
SRR2169558 branch tip branch tip not recorded not recorded SRP062488 17.00
SRR3223317 branch tip branch tip not recorded not recorded SRP062488 15.74
SRR3169421 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169518 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169528 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169533 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169535 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
SRR3169538 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169539 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169540 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3169541 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182410 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
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
SRR3182781 branch tip branch tip not recorded not recorded SRP062488 0.00
SRR3182786 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 correlated8agem_s0167.g2.t1-0.263752740618655

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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