Gene detail

Detailed information of BRAKERMNPP00000003416.1 in Nemopilema nomurai

Genomic Location: scaffold17:369324...387771
NR annotation: XP_020624000.1, forkhead-associated domain-containing protein 1-like isoform X1 [Orbicella faveolata]
Species Nemopilema nomurai · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERMNPT00000003416

atGTTGAAGACACCAGATTTTTCACATTTAAGTAAGGAATATTCTGAAGATGTCTATGAGCCTGCAGAGGACACCTTCTTGATGATGGATGCATTAGAGGCCGATCTTCCATTCATAACCAACATTAGGCCATCGATTTGCCTAGAGGTGGGATGCGGTTCAGGGATCACATTGACGTCCTTAGCAATGGCTTTAGGAAAATCTACATTTTATCTTGCTACAGATATAAACGAAAAAGCTGGAAGCTGCACATATTTGACAAGCAGAGCTAATTGTGTTGACATCGACATTGTAGTTGATGATTTGGGAAGTGCCCTTCTGCCAAGACTCCAGGGTTTAGTCGACATTCTTGTATTCAATCCGCCATATGTAGTAACTCCGTCAGAAGAAGTCCACAGTAGATCAATAGAAGCTTCGTGGGCAGGAGGAATTGATGGAAGAGAAGTGATTGATAGGTTTTTGCCAATTGCTGCCAGTTTGATCTCAAAGACAGGTGCACTGTATATGTCACCAGTGATTGACAAAATACATGCAGTTATTTATGCTGATGAACCAGAAAAGGCCTATGCAATACGGGATCTCAACACAGCCCATGGAACCTATGTCAATGAGTGCAGGGTACAGACCGCACCAGTAAGGCTAAAAAATGGTGATGTGATACAGTTTGGGTTCAGTGGACCAATCTTTGATTTAAAAGTAGAACCTGGTGCATTTTACTCGCCTGCTCATCAAGCATGGAACTTGTCACAGAATTACCATGCAGAAGTGGCCCAAGACACTACACATTTGCCCCCGATAGCTGTCCCAACTGCTCCAACTGTGCCAAATTACCAGTATCCAGCAGCAAGTAGCAGCTTGCCATATCCACCAGTTGGGCATGTACCTCAACAAACATATTTTGATACAAAGCCACCGGCCACTGAAAATATCATACCACACCCTCCACTGCCTGGCAGATCCATGTCTGGCAAACTGTCACGACCACTGTCAGCTGGAGGCCTCTCGTCTTCAGGTCGATGGATTTTTAGTAAAAGCATTAAGGACATGACTTcagaagaaaaagcagaagagATGGAGCAACAGTTGCTGAAGATGGGTTATGAAGTAAGACGGCTCGCCTCATTTGAAACGGAATGTCATCGCAAGGACAGTGAAATCGTTAGTTTGCGCAACGAAATAGTAGATCTGCGGTCGATTTTGAGCAGAAAGGATGATGAACTGCACAGGTCTGGGTTGGAGTACAAGTATCATAGCGAGTCTATATACTCGCAGCACGACTCCGATATGTTGAAAAATGTCATCCAAGAGAAGGAGGAGTTGAAGAGGCATAGCGCACATAAACTGGCCTTGATGCAAAGCCAGTTAAACCAGAAGAATAAGGCAATTAAGGACCTGGAGGATAGACTTGACGTTCTTGCTGGCCAATCATCGAGACCATACCAAGAGCAGTCCACTGACGTCATTGCTTCATTGAAGTCGGCAATGGCACACAAGGACCTTCAGGATGCACTTGTCcagaaaaataagaatgaaaatgataGATTGAGGCGGGATATTCGAGAGAAAGAAAACCAGATTGCATCGCTATCTGCTAAGCTCACCAAACAGAGGGCAAGCAAAGAAGCAGAGAAGGATTTCCGAAGAAAGGAGGAAGAGCTTGGCAGCTTTAGACAAAAACTACTAAATGCAGATCACCAAATTCAGGAGAAGATATCAGTAATacacaaaatggaaaatgaaattgaaaacttgaagagaATCATCGATGAAGACAAACAGAATGATATTCATATGCAGAAGGAATTGCAGAACATGCGAATTCAGTATGTCGAAAAAGAACGTGCCGACAAATCAAATCGAGTAGAACTCAaggaaattcaaattaaaCGAGACAAGTTTAGGAGTGACCTTCTGCGTATCCTATACTTGAGTGGGCTTGCGAAACCTGACGCCGAAATGTATGAAGAAGATTTCATTAGAGCAATCGAGCAAATAATCGAAGAGAGGTCAAACCTGAAGTCAAGAGCCGACGAGTTAAAGCACTACGCCAAGGAAGACGAGCATTGTAGACACTCCCTTGAAAAGTTCTTTGTGTCGATGCAGAAAAGATTGATAAGAAATGGCCGGCTTTGTGAATCCCTTGATGACGAGCTAAGGGGCATTCATGATGTAGATGTTACCAACAATTTGGCATGGATGAAGGATGTTGTTGCTGGTATATTGGAGCAAGAACGTAATTGGGAGCAAGGAATTGAGGATGCATTGCAAGATGCTGGCATGGAAGTTGACAGAGGAAAGAATGAGCCTTCTCATTTGATTAGAAAAATGAAGGAACGGATGATgaagaaaaaggagaaaatcGTCCACTTGAAAACAAGATTGAAAGCTGTAGAAGGTGAGCACGAAGAATCTCTGAAGAACTTTAAGATCAAGTTTCTTCGCGAGACAGAGGATGAGGTCACTAAGGCGGTAGAAAAGTTGAAGATCGGCGAAGAGAAGAAGATCCAAGAACTTAAGCATGAATTTTTGAGGCGAGAGAAGCAAAAAGTTGCTGAAGCGATTGAGACAGAAAGAAAAGTCTTTGAGAGGGAATTTGGAAATCTCACCGAACTTCACAAGCAATTAGGCCAAACGCATCTCGTAATTGACCAACAAAAGAGCAAATCTAATACATTGGAAGATCAGGTTCTGCAGCTCAAGTTTGCAATGGAAAAGGCCCAGCAAAACGAGAATGAATTGAGGAAAGAAATAGAAGAACGCGACGTGAATCACAAGGCACAGCTGGAAGCTGTAAaccaagaaaaggaagaagtaAAGCATAAGTGTATCGAAGAAATCAGTGTCCATAGAGAGCAATCCCACCAATACAGTCTGACAATCGTTGCTTTAGAAGATAAACTATTGAAGCTGAGCAAAAGCAGAAGAAAGACGGATGATGATCTCAGCTACTTGAAGCAGTATAGAGATTCCTTTTCGCTTACAAACAAAACTTCACCAAGACCAAAGAGTCCAAAAAGAATGGTATCAAGGCCAACATCTCCACGAAAGGTCCACAAAAGAGACGCTGCAAATTTGACCGACCTGTCACTGTTGGAGCAGGATACCCggagaaaagaagaagttgAAAGGCTTGAGCAGCTAGTTATTGCTCTCAGgaAAGAAGCAAATGAGGCGAGACGGCACACCAATGAACAATCTGAAGTCGTAAAAGGATTGAGACGCGATCTGGCTGGAGCTTCAGCTAGGCTTTCGGATATCACAGGGGAACTTGATGATACTCAGAAGCAGAAGATCGAAGATTTGCAAACTCGAATCGTGaaacaagacgaagagctGTTTGGGCAGAGGAAGCAGCTTGCCGAATTGTCAGCACTTCTGGAGAAGCAGAAGGTGGAGCTGCTGAAGAGGGACGGGAAGCTGAAGGAGCAAATGTTTGTCACAAAAGAACAGGACAAGAAGCTGAAAGAAAAGGGGAAGGAAATTGTGCAGCTGATAAGGTCACAAGAGGACAAAGAAGTGGAAGACGACGCAGAGAAGTTGCAAATCGTAAAGCAGGCTTTCGCAAGCCAAGAAGTCGTGGCAGCAGGAGCCCGTTGTCTTGGCGACAAACATGATCAAACAATCACCAGGCAAAGAGAGGCTATAGCCGAAATGAGGACGAGGATTAGAGAGCTAGAGCAGTTTCAGCCACCTTACCCGTCCCAGCAAGCGGCTTTGCAGCAAGTTGGCATCATGAAGCGGGAACTGGCTGAACTCAGAAGCGAGCTTGCAGTCAGGGAGCAGGACATGTACAAAGACGAGACCGAGTTGCAATCGGAGACACGAATGTCCCGCGAGCTTCTTAACTCTGTGAATCAAGAACTTGCCGTTGAGAAACTTGCTCATAATGATACAAGGGATTCACTGGATATCAGCGAACGCATATATATGGATTTGATGCGAGCCGTTTGTGGGCTGTTGGACATGGAGATGCCAAAAAAGATCGGAACGATGATGCACTTACCTCccaaagaaaaagagaaattgaTCAATGAAAGGAACAGGGTTCTAGAGGATGTAATCAAAAGACTAGATGCCCTGCAGAGGAGACTTGGTCGAAAGGAAAAATTACTTGGTGGTTATGAAAAAGACTTAACCCAATTAAGAGAGACTGAAGAACTGGTGGGAAGAAAATCGGCAGAGGCGACTTCATTATCGACGTCTCTTCGaagtaaacaaaatgaaattgacTGCTTAAGGGAAGCCCTCAAGAGAGTACGTGAAGAGCTGGACCAACAAAAGCGATTGAACAAGTCACTATCGCAAAGAAAGGTTTTTAAGATGGACCTAGATCAACAGCGCGAACAGGAATCGCGAGGACATAGCTGCCATGAAGATGACGAAAAACGGCAAAAGGaggaaatgaagaagaaaaagcaaaatgaaaagttaaaaCGCAAGAGTTATGAAATCGAATCTCTTAAAAAGGAACTTCGTTCAGCTGATCTAGAGCTTAGTGAAACTGCTGCGAGACTTTACGAGTTTCAAACAAATCAGAGTCGACCAAGTCCTTGGTCGGATTCTTTAAAGGAAGAAACAGAGCCTGCTCTGGAGGAGCTTTGGAAGCATTCGTAG

Transcript

BRAKERMNPT00000003416

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6SKR2	Methyltransferase HEMK2 OS=Mus musculus OX=10090 GN=Hemk2 PE=1 SV=1
Q9Y5N5	Methyltransferase HEMK2 OS=Homo sapiens OX=9606 GN=HEMK2 PE=1 SV=4
A6PWD2	Forkhead-associated domain-containing protein 1 OS=Mus musculus OX=10090 GN=Fhad1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001080 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00498 all species →	FHA	FHA domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR052642 all species →	Family	Coiled-coil and Forkhead-associated domain-containing protein	Interproscan
IPR000253 all species →	Domain	Forkhead-associated (FHA) domain	Interproscan
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR002052 all species →	Conserved_site	DNA methylase, N-6 adenine-specific, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR18853 all species →	FORKHEAD-ASSOCIATED DOMAIN-CONTAINING PROTEIN 1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0032259 all species →	Biological Process	methylation	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

No KEGG orthology assignment for BRAKERMNPP00000003416.1.

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

Co-expression network

Genes whose expression across the transcriptome samples of Nemopilema nomurai 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Nemopilema nomurai, 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 →