Gene detail

Detailed information of XP_068735005.1 in Montipora capricornis

Genomic Location: chr2:63891786...63906364
NR annotation: XP_029185006.2, small RNA 2'-O-methyltransferase-like isoform X2 [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068878904.1

CTCCCGCCAAAAGGGAAAATGGCGGCAAGGTGTTTGAAATACTGAAAAGTTATCGAGTCATCTTTCAACTTTTCTGTGACTTCAACTGAAAACTTCCTGTTTTATGTAAGTTGGAGTGAAGCTTTGAAActtcaaaatgtggtaagcaATGTGAAGCAATGAATGCTCTCGAGGCCACAAGTGGCAACTTTTCTGCTGGGCTTAAACATGAAAGTGAAACTAAAAGTGAATTGGAGAAACAATTTGAACACGGACATCGGACAGAGGCTGAGGAAGCATTCCAAGGTCCGAAATTTGATCCCCCAGTTTACCGTCGAAGATACGCTGCCGTTTGTGAGCTTGTAAAGAAACACCAAGCGAAAAAGGTACTTGACTTTGGGTGCGCTGAGGCAAAACTCGTGAAAGTTTTAATAAGTCAAGAGCAGTTGACTCACTTGGAAGAGGTGGTGGGTGTGGATATTGACAGGGAACTTTTAGAGAGGAATGAATTCCGTATAAAACCTCTGATATCAGATTATCTGAGACCCCGCAGTCATCCGTTCAAAGTCTCCTTGTATCAAGgttCAGTCTCTGAAGCAGATGAGAGATTTGTTGATTTTGATGTGATTGCTTGCATTGAGCTAATAGAACATCTTGAACCTGAAGCACTACATTTAATGCCTGAAACTGTTTTTGGTCAGCTCTCACCCAAGGTTGCCATTGTAACAACACCCAATGTTGAGTTTAATGTGTTGTTTCCAAATCTCCAAGGATTCCGTCATTATGATCACAAGTTTGAATGGACTAGAGCTGAATTCCAAGAATGGTTAGTTGCGTCTTCAGATAGGGGTTGTTTACATGCAGGAAGGAAGATGGCCAACACCCAAGCCAGCAGATACAACTATTTTGTGACATTTGATGGCATTGCTTCTGGACCAGTCGGCACTGAGCATTTGGGTTGCTGTTCACAAGTTGCTGTATTTGAGAGGATATCCGTGTCTCCAAATGCTTCAAAAGTACAGCAGCCTTACAATCTGGTTGCAGAGGTTGAATACCCTTTTAGAGTGGACACACGAACTGAGGAGGACAAAATCTTGCAAGAAGTGGAATATATCTTGTGGTTATTGTCATCCCAGaaggaggaagaagaggaaaacaGCAGCAGCAATTCCACACTCAACAATGAGGATAACTTGGATGGTCATCTTGGAGAGGAACACACCGAAGATAAATATAGTAGAGATACAATAGGGGCTGAAAATAATGAAGCTCGTGTGTACCCTCTAGAAAAGCTTCTCAGCTTTTCTTGTCTTTGTAATGTATGTCAAGACATCAACAGGCTCAGAGACGTTCTTCAGGATTCCTCATTATACCAACTTACTGAGGATGGACTTGGTGTTCTGTGGCAACAGTCATCTCCCTGTTGGAGTAGTGATGAAAATGACACAAATTGGGATGACTGTGATGATGCCTTGAATTCTAAAGAATCTGAGTTGGACAAGCCTGAAAACTGGGATGATGACATTAGCAGTGGTGTCTGTGGAGCCGGTGAAGTAAACAGGATAAACCCAGCAATTTCATTTACAAAAGAATTATGCTGGAATGATTCGAACAACTGCGCTAAATTATGGAATGGCAAGGACTGGAGTGAACTTGATGATGAAATAACTGAAGAAAATATAGACGAGGAATTTGACTCCAACTTAAATTACTGGGACAACAAAGTCGTAAAACAAGAAAGTGATGCATCTCATAGCAATGATAGTGATGATGGTATTACAGATgatcttttttggatttcacttgAAAGCTGATGATGCAAGTCACATCAAACTAAAAGAAGACAATGTTTAGAAGACCTTGAGAGTACTCTTGCTGTTGGACTGAAATAGTCACACAGCAGATTCTTGTATGGCCAGATTACTTGCAGCAGATTATTTGCTACTgcattagctttcattttgtgtttcTTCACTGAACCAGTCCAACTGTACAATACAAATTAATGTGTATTCCTCttctgttttgatgtttcctAAACTCTTGGCTATGCAAAGGGTAACATATCTTTTTTCTTCATGAAATGGTTCCTGTTGAGGATAGGCttaaaatttctctttaaaTTGTAGACAGAAAAAGCCTGTATTCTGTTTGGGTCGAAAAACCTGATGcgcattttaatgtttttaacaGCTTGTAAAATTAACTCACGTTTGCTTTTACGAGAGTTTAATAATgtaataaaaacgttttgttaCCCCATCC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7K175	Small RNA 2'-O-methyltransferase OS=Drosophila melanogaster OX=7227 GN=Hen1 PE=1 SV=1
Q32PY6	Small RNA 2'-O-methyltransferase OS=Rattus norvegicus OX=10116 GN=Henmt1 PE=2 SV=1
Q8CAE2	Small RNA 2'-O-methyltransferase OS=Mus musculus OX=10090 GN=Henmt1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005302 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13847 all species →	Methyltransf_31	Methyltransferase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR026610 all species →	Family	3'-RNA ribose 2'-O-methyltransferase, Hen1	Interproscan
IPR025714 all species →	Domain	Methyltransferase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21404 all species →	HEN1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0001510 all species →	Biological Process	RNA methylation	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008171 all species →	Molecular Function	O-methyltransferase activity	Interproscan
GO:0008173 all species →	Molecular Function	RNA methyltransferase activity	Interproscan
GO:0030422 all species →	Biological Process	siRNA processing	Interproscan
GO:0034587 all species →	Biological Process	piRNA processing	Interproscan

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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K20798	HENMT1; small RNA 2'-O-methyltransferase	EC:2.1.1.386	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068735005.1 across 36 RNA-seq samples of Montipora capricornis. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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.

36Samples

0TPM > 0

1Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	0	0.00	0.00

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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 Montipora capricornis 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	0	not in this network	-
Negatively correlated	0	not in this network	-

This gene has no edge at all in the Montipora capricornis network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.

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 Montipora capricornis, 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.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search 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 found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look 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 analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →