Detailed information of asel_s0129.g16.t1 in Acropora selago

Genomic Location: sc0000129_pilon:232625...235335
NR annotation: XP_029192330.2, repulsive guidance molecule A-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
Q8JG54Repulsive guidance molecule A OS=Gallus gallus OX=9031 GN=RGMA PE=1 SV=1
Q96B86Repulsive guidance molecule A OS=Homo sapiens OX=9606 GN=RGMA PE=1 SV=4
Q6PCX7Repulsive guidance molecule A OS=Mus musculus OX=10090 GN=Rgma PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008115 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF06534
all species →		RGM_CRepulsive guidance molecule (RGM) C-terminusFamilyInterproscan
PF06535
all species →		RGM_NRepulsive guidance molecule (RGM) N-terminusFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR009496
all species →		DomainRepulsive guidance molecule, C-terminalInterproscan
IPR010536
all species →		DomainRepulsive guidance molecule, N-terminalInterproscan
IPR040287
all species →		FamilyRepulsive guidance moleculeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR31428
all species →		RGM DOMAIN FAMILY MEMBER DRAG-1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005886
all species →		Cellular Componentplasma membraneInterproscan
GO:0015026
all species →		Molecular Functioncoreceptor activityInterproscan
GO:0030509
all species →		Biological ProcessBMP signaling pathwayInterproscan

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
No KEGG orthology assignment for asel_s0129.g16.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of asel_s0129.g16.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
24TPM > 0
1Conditions
72.0Max TPM
46.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
coral larvae 24 24 45.97 72.05

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR14308015 coral larvae coral larvae not recorded not recorded SRP315987 72.05
SRR14308021 coral larvae coral larvae not recorded not recorded SRP315987 70.90
SRR14308008 coral larvae coral larvae not recorded not recorded SRP315987 64.45
SRR14308014 coral larvae coral larvae not recorded not recorded SRP315987 61.53
SRR14308018 coral larvae coral larvae not recorded not recorded SRP315987 60.88
SRR14308012 coral larvae coral larvae not recorded not recorded SRP315987 57.97
SRR14308026 coral larvae coral larvae not recorded not recorded SRP315987 53.67
SRR14308006 coral larvae coral larvae not recorded not recorded SRP315987 52.55
SRR14308022 coral larvae coral larvae not recorded not recorded SRP315987 51.44
SRR14308016 coral larvae coral larvae not recorded not recorded SRP315987 47.75
SRR14308024 coral larvae coral larvae not recorded not recorded SRP315987 45.98
SRR14308013 coral larvae coral larvae not recorded not recorded SRP315987 44.79
SRR14308011 coral larvae coral larvae not recorded not recorded SRP315987 43.91
SRR14308004 coral larvae coral larvae not recorded not recorded SRP315987 43.69
SRR14308025 coral larvae coral larvae not recorded not recorded SRP315987 42.85
SRR14308027 coral larvae coral larvae not recorded not recorded SRP315987 40.28
SRR14308005 coral larvae coral larvae not recorded not recorded SRP315987 40.00
SRR14308019 coral larvae coral larvae not recorded not recorded SRP315987 35.82
SRR14308010 coral larvae coral larvae not recorded not recorded SRP315987 33.76
SRR14308017 coral larvae coral larvae not recorded not recorded SRP315987 29.91
SRR14308007 coral larvae coral larvae not recorded not recorded SRP315987 29.31
SRR14308023 coral larvae coral larvae not recorded not recorded SRP315987 28.96
SRR14308020 coral larvae coral larvae not recorded not recorded SRP315987 26.08
SRR14308009 coral larvae coral larvae not recorded not recorded SRP315987 24.85

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 correlated10asel_s0275.g15.t10.823517970324884
Negatively correlated20asel_s0020.g17.t1-0.785965982521471

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 →
TOP