Gene detail

Detailed information of ENSODKP00000038355.1 in Millepora complanata

Genomic Location: chr8:147233319...147301234
NR annotation: CAH25437.1, HyFMR1 protein [Hydractinia echinata]
Species Millepora complanata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSODKT00000041660

ATGGATGATGTTAAAGTGGAGGTCCGGAATAATTTGAATGGTGCTTTCTTCCCGGCAGAAATAAAGAATATTCACTCAGAAGAAGCGACTATTGCCTTTGATCACAACCCAGAAAAATGGCAGCGTGTTCCTCTACAAGATGTTCGAAAGCCTACTCACTTTACTAGAGACGCTTTAAAGTTCAATGAAGGAgatgaaattgagattttttcaaaagaagatgaaacagaGCCAATGGGATGGTGGAATGGAAAGGTGGTGTATCGAAGGGGAGGCTTCTTCGTAGTTAGTTTTAATGGGTTAGATGAAGCTTTTAATGAAATCGTGCCCCTAGAAAGAATACGGCCCCCGGGACAATGGATTCCAGTTACACGATCAATGTACTTCAAATGCATGATTGACGTACCCCAGGATTTGCGTGGAATatgtgCTACAGATGTTCATATCACTTTCTGTTCGCAAACCAAGGCAGCTTCTGTTTTCTATCACTCAGATCTTAATGTATTGGTCATTCTTTCGACATGTGAAGAATCAATTAAGAAGGCTGCCATTTTAAGTGAAATGCATTTTCGTAGTCTGCGCACTAAATTGTTATTACGATCAAGAAATGAGGAGGCTATGAAACAGCTAGAGGCAGCAAAGAAGCAGGCGCTGCAATCACCTATATACGAACAGCTTACTTTACCTGAAGATTTGGTAGGACTAGCAATCGGGGCACAAGGGGCAAACATTCAAGCTGCAAGGAGGATTCCTGGTATTTTATCAGTCGAAGTTGATGAACCAGCTTGTACATTTAATATACTTGGAGAGAATTTAGAATGCGTTCGAGAAGCCCGCCGTTTGTTAGAATTCGCAGAAGAGCAAGTGCATGTGCCAAGAGTTTATGTTGGGAAAGTAATCGGTAAGAACGGACGAATTGTGCAAGATATTGTTGACAAATCGGGTGTTGTTCGGGTAAAAATTGAACCTGAACCAGAACAAGATAAATCCGTGGAAGAAAAACAGAAAGACGTTCCGTTCCTGTTTATTGGGACACGAGACAACATCGCCAATGCAAAGATGATGCTTCAATACCACTTGATCCATCTCAAGGATGTTGAGGATTTACGAACAGAGAAAGAGAAGATTGATCAAGAGTTACGCAACTTCGGTGTCAGCCCTCCAACGGGTCCATTCTTTCCACCACCGGCTGAAATGCGACGCCAACATGCTTTAAGTATTACTTCACAAGATGTTAGAGACCGAACTCAAACGATTGATAGTTACGCTGGTGATTTGGATGAACTTCCAATTTACACAGCAAACATCAATAAAAATCCAACGTTTGGACTGAGAGTGAGAACGTCAAGTGAAACAGAACCGTTGAAAAAGGAGGAAAAGCATGGTCGTATTTCACCAAATATGAAACTCTCACCAGAGGGAGTTCCCCAAACAATCCCCGAAGCTGAAGCAGAATACGCGAATGAAAATAAGAAGGGCCCTAGTCAAGTGTCAGTCCGAGGTCGTGGTTCTTCTTCAAGACGTGGCTCATATAATAACCATGGCAACAGACAGCCGCAGGGTACGAGGCAACGTGTGAATAGCGAAAGTGAACGCAGCAAAGCAAACGAAGACTTAGACTGGCGCAATCACGGAGATATACCCACAACTAATAACCAAGGGCAGTCTCATTTTCCACCGCAACGAAGGAGGACAAAAAGTGAAGGGGAACCTCTACCAGACCAAAAGCCCGTTCAAATCAAACAGCGATCTACAACCACTATTGGTAGTCAGCAACCTTACCACAACAAACAGGGCGATAACAAACATCAAGCTAAACATCAAAAAAGCGATAATCGTTATCCGCATCACCATCATCAGCAGCAACATTATCCTAAACATCAGCAACAAAACCAGCACAAAAATCAGAAAGGAAATCAGCAAAACCGACCTAATCCACCTCGTGAACATCGAAAAATGGTCCGCCATGCTAATAACCCAACCAAAATTGCTCAAAACAAATACTCAAAAGAAAAGTCAGATTCAAAAGATGAAAGTTCAAAAGACGATGCATCATCATCTGCAGTATCGAATGAAACAGAACAGCAAGTAGTTTCTGCAGAAGCTAATAAAGAAGTCGAACGTCCCGTCAGCGTTACAGTCATAGACGAGAAACCGGTCACGGAACCCGATTTAACGGAAGGCGTTGTAACCAACAATGAAAGTACAGCAGCGATCGTTGAAAGTACTGTTGTGCTTGAAGATAagaataaaaacgaaataaacgATCTTAAAGATGTATCATCAACAAATGGACcttctattgaaaatgatgtaattCTCGATAGTAAACCAAAAGACTCCATTGTGGAGGAAACGAAAGAAATTTCCCCACCACAGGAAGCAaactag

Transcript

ENSODKT00000041660

CATATCTCTAGCCATGTTGGCAAATAACCCTGAAATGAGTAGGCTTAAGGGAAGGTTTTTGTTAAAGTACCCTGGTGTGGTTGCCGGATCATAACAATAACTCATTTCCCTAACAAGCGTGGAAGTTGTAAACATGGATGATGTTAAAGTGGAGGTCCGGAATAATTTGAATGGTGCTTTCTTCCCGGCAGAAATAAAGAATATTCACTCAGAAGAAGCGACTATTGCCTTTGATCACAACCCAGAAAAATGGCAGCGTGTTCCTCTACAAGATGTTCGAAAGCCTACTCACTTTACTAGAGACGCTTTAAAGTTCAATGAAGGAgatgaaattgagattttttcaaaagaagatgaaacagaGCCAATGGGATGGTGGAATGGAAAGGTGGTGTATCGAAGGGGAGGCTTCTTCGTAGTTAGTTTTAATGGGTTAGATGAAGCTTTTAATGAAATCGTGCCCCTAGAAAGAATACGGCCCCCGGGACAATGGATTCCAGTTACACGATCAATGTACTTCAAATGCATGATTGACGTACCCCAGGATTTGCGTGGAATatgtgCTACAGATGTTCATATCACTTTCTGTTCGCAAACCAAGGCAGCTTCTGTTTTCTATCACTCAGATCTTAATGTATTGGTCATTCTTTCGACATGTGAAGAATCAATTAAGAAGGCTGCCATTTTAAGTGAAATGCATTTTCGTAGTCTGCGCACTAAATTGTTATTACGATCAAGAAATGAGGAGGCTATGAAACAGCTAGAGGCAGCAAAGAAGCAGGCGCTGCAATCACCTATATACGAACAGCTTACTTTACCTGAAGATTTGGTAGGACTAGCAATCGGGGCACAAGGGGCAAACATTCAAGCTGCAAGGAGGATTCCTGGTATTTTATCAGTCGAAGTTGATGAACCAGCTTGTACATTTAATATACTTGGAGAGAATTTAGAATGCGTTCGAGAAGCCCGCCGTTTGTTAGAATTCGCAGAAGAGCAAGTGCATGTGCCAAGAGTTTATGTTGGGAAAGTAATCGGTAAGAACGGACGAATTGTGCAAGATATTGTTGACAAATCGGGTGTTGTTCGGGTAAAAATTGAACCTGAACCAGAACAAGATAAATCCGTGGAAGAAAAACAGAAAGACGTTCCGTTCCTGTTTATTGGGACACGAGACAACATCGCCAATGCAAAGATGATGCTTCAATACCACTTGATCCATCTCAAGGATGTTGAGGATTTACGAACAGAGAAAGAGAAGATTGATCAAGAGTTACGCAACTTCGGTGTCAGCCCTCCAACGGGTCCATTCTTTCCACCACCGGCTGAAATGCGACGCCAACATGCTTTAAGTATTACTTCACAAGATGTTAGAGACCGAACTCAAACGATTGATAGTTACGCTGGTGATTTGGATGAACTTCCAATTTACACAGCAAACATCAATAAAAATCCAACGTTTGGACTGAGAGTGAGAACGTCAAGTGAAACAGAACCGTTGAAAAAGGAGGAAAAGCATGGTCGTATTTCACCAAATATGAAACTCTCACCAGAGGGAGTTCCCCAAACAATCCCCGAAGCTGAAGCAGAATACGCGAATGAAAATAAGAAGGGCCCTAGTCAAGTGTCAGTCCGAGGTCGTGGTTCTTCTTCAAGACGTGGCTCATATAATAACCATGGCAACAGACAGCCGCAGGGTACGAGGCAACGTGTGAATAGCGAAAGTGAACGCAGCAAAGCAAACGAAGACTTAGACTGGCGCAATCACGGAGATATACCCACAACTAATAACCAAGGGCAGTCTCATTTTCCACCGCAACGAAGGAGGACAAAAAGTGAAGGGGAACCTCTACCAGACCAAAAGCCCGTTCAAATCAAACAGCGATCTACAACCACTATTGGTAGTCAGCAACCTTACCACAACAAACAGGGCGATAACAAACATCAAGCTAAACATCAAAAAAGCGATAATCGTTATCCGCATCACCATCATCAGCAGCAACATTATCCTAAACATCAGCAACAAAACCAGCACAAAAATCAGAAAGGAAATCAGCAAAACCGACCTAATCCACCTCGTGAACATCGAAAAATGGTCCGCCATGCTAATAACCCAACCAAAATTGCTCAAAACAAATACTCAAAAGAAAAGTCAGATTCAAAAGATGAAAGTTCAAAAGACGATGCATCATCATCTGCAGTATCGAATGAAACAGAACAGCAAGTAGTTTCTGCAGAAGCTAATAAAGAAGTCGAACGTCCCGTCAGCGTTACAGTCATAGACGAGAAACCGGTCACGGAACCCGATTTAACGGAAGGCGTTGTAACCAACAATGAAAGTACAGCAGCGATCGTTGAAAGTACTGTTGTGCTTGAAGATAagaataaaaacgaaataaacgATCTTAAAGATGTATCATCAACAAATGGACcttctattgaaaatgatgtaattCTCGATAGTAAACCAAAAGACTCCATTGTGGAGGAAACGAAAGAAATTTCCCCACCACAGGAAGCAaactagaaatttttaaaaagtagattttagttttttctcattttttattgttacatataacgctctttgaaaatatattaagcaTGCAGTATAACCTGGGCTTGATCTGATAgggaaataaattttataatttaatgacCAAAGCATCTTTCTTGTTTATATTAGGTATACATTTCTGTGAAATGGGACAACAAGTTTTATTTGTATTAGGGCATACG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P51115	RNA-binding protein fxr1-A OS=Xenopus laevis OX=8355 GN=fxr1-a PE=1 SV=2
P51113	Fragile X messenger ribonucleoprotein 1 homolog A OS=Xenopus laevis OX=8355 GN=fmr1-a PE=1 SV=1
Q7ZTQ5	RNA-binding protein fxr1-B OS=Xenopus laevis OX=8355 GN=fxr1-b PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005946 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17904 all species →	KH_9	FMRP KH0 domain	Domain	Interproscan
PF18336 all species →	Tudor_FRX1	Fragile X messenger ribonucleoprotein 1, Tudor domain	Domain	Interproscan
PF00013 all species →	KH_1	KH domain	Domain	Interproscan
PF05641 all species →	Agenet	Agenet domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036612 all species →	Homologous_superfamily	K Homology domain, type 1 superfamily	Interproscan
IPR040472 all species →	Domain	Synaptic functional regulator FMRP, KH0 domain	Interproscan
IPR041560 all species →	Domain	FMR1, tudor domain	Interproscan
IPR004088 all species →	Domain	K Homology domain, type 1	Interproscan
IPR008395 all species →	Domain	Agenet-like domain	Interproscan
IPR004087 all species →	Domain	K Homology domain	Interproscan
IPR040148 all species →	Family	Fragile X messenger ribonucleoprotein 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10603 all species →	FRAGILE X MENTAL RETARDATION SYNDROME-RELATED PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0003730 all species →	Molecular Function	mRNA 3'-UTR binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005844 all species →	Cellular Component	obsolete polysome	Interproscan
GO:0006417 all species →	Biological Process	regulation of translation	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0017148 all species →	Biological Process	negative regulation of translation	Interproscan
GO:0036464 all species →	Cellular Component	cytoplasmic ribonucleoprotein granule	Interproscan
GO:0042803 all species →	Molecular Function	protein homodimerization activity	Interproscan
GO:0043488 all species →	Biological Process	regulation of mRNA stability	Interproscan
GO:0045182 all species →	Molecular Function	translation regulator activity	Interproscan
GO:0045727 all species →	Biological Process	positive regulation of translation	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
K15516	FMR; fragile X mental retardation protein	-	Messenger RNA biogenesis	ko03019	deepkoala

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 Millepora complanata 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 Millepora complanata, 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 →