Gene detail

Detailed information of ENSSYXP00000013310.1 in Micromussa lordhowensis

Genomic Location: chr3:10000485...10052116
NR annotation: XP_020625960.1, nuclear cap-binding protein subunit 1-like isoform X1 [Orbicella faveolata]
Species Micromussa lordhowensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSSYXT00000014074

ATGTCCAGGGAGAAAAGGAGATATCAAAGTGAAGATGAAGaAGGAAGAACACGGAAGCGAAGAAGAACAACAGAAGTTGTGGATATTGAAGACCGTCTAGAATCTCTTATCACACGTGTAGGAGAAAAGAGTACATCATCTCTTGAAAGTAATCTGGAAGGTCTTGCCAGTGTGCTGGAAGCTGATTTGCCTAATTACAAAGAACGCATCCTCAAGATTATTTGCACATGTGCTGCAAATCTACCAGAGAAAACAACTGTTTACAGCACACTAGTAGGACTTTTAAATGCAAAGAACTATGGATGTGGAGAGGAGTTTTTAGACATGATTCTGGAAAATCTCAAGGAAGTGCTGGTTGCTGCTCAGTTTGACAGAGCTAGATTGATGGTGCGGTTTCTTGCTGATCTGGTGAACTGTCGTGTTCTCATGCCTAGTGCACTTTTAGAGTTTTATGACAAGCTTCTGGCTGCTACCTTGGAGGAAAACATAACACAGGTTCGATCTGACTGGTTTGTGTACATGGTACTATCTTCGTTGCCCTGGGCTGGCAAGGAACTTTCAGAGAAAAAGGGTCAGGAATTTGAACAGCTGTTATCAACTATTGAGCACTATATAAGTCATAGACACAAGACTCACATTCCTTCGCTCCGAGTGTGGTCAAAAGATGAGCCTCACCCTCAAGAGGAGTATATGGACTGTCTGTGGGCACAAATCAAGAAACTGAAATCTGACAATTGGCAGGAAAAACATATCAGGAGACCTTATCTTGCATTTGATGATGTTCTTGGAGACGCTTTGCAGCATACCCTTCCATCATTCATGCTTCCAGTACTAAAGGATGGCATTGTATACCCTCTTCCAAAAGTAGTTTATAGAATGTTTGATTACACCGATGTACCTGAGGGTCCTTCCATGCCAGGAGCCCATGCAATTGAAAGATACTTAGTAGAGGAGGGTATTGAGAGAACAATACATGCACATTTTAAGGACAGAAAAGAATGTGCAAACCAGCTATTAAACTTGCCTGGAAAGTCTAAAGTACCAATGCATTACTGCATTATTGAGGTGATCTTTTCAGAGATGTTCAAACTTCCAAACTCACATCATCCCCAAATATTCTATGGCGCTTTAATTATTGAACTATGCAAATTACAACCAAATTCAATCCCTGGCATTGTTGCCCAAGCAACTGAACTGTTGTATGAGAGATTAAACTCAATGAACACAACTTGCGCTGAAAGGTTTGTCTACTGGTTGTCATATCACCTCAGCAACTTTCAGTTCAAATGGGGCTGGGACGAATGGGTTTCTGCCACTGATGATGGATTGGATTCACCTAAATGTACTTTCTTGAGTGAGCTGTTCGAAAGGATAAAAAGATTATCATACCATCAATTTCTGATTGAGAACATTCCTGAAGGATTGCATACCCTCCTTCCCGTTGCTCCTGCATCAAACTACAGATTCACAGAGGAACAAGGAGAGTTACCAGGAGCAGATGTCGCCAAAAACCTACTGGAAGCCATCAGAGCTAAGAAAGATGTAGATCAACTTCAGACCATTTTAAACAACATACCAGCAAATGCAACTGGTCGTGAGGACTTTAATACTGATGTGCCAGTGATCGACCACACTTTCCCACAATTAAGACTAGAGGTCTTGCTTCAGGTTGTGCTCAAACTTGGTTCCAAATCGTTCAGTCATTCTTTCAGTGCTCTAACGAGGTTCCACAAACTTCTTAAAAATGTCATTGTGAACGAAGAAAGTCAGATACATTGTCTGAAGATTGTGAATGAGTTTTGGTCCACAAATCCTCAGATGATGGTGGTGTTGGTAGATAAACTGGTACGCATGCAACTCACTGATTGCTCAGCAGTAATCAACTGGCTTTTTTCCAAGGACATGAAAGATAACTTCACAAAGTTATATGCGTGGGAAATAATGACAGGCACCTTAAAGAAAATGAGTAAACACACCAATAAGGTGTTGGGTGAAGTACAAGAAGCCAAAGAAAAGCTGACAAAACTGgaagaaaaagctaaaaaacAGCCTGGAGAAGCAAATGGTGATTCAAAACCTGACCCATGTCCAGAGGAAGAATTGGATAAAAAGCAGCAACAACTAGAAGAACTTACAGAAAAATTAGAAAATGCTCAGAGAACTCAAAAACAACTCTTCCTTATTGTTTTCCAGCGTTTCATCATGATCCTTACAGAACACATTGTGCGTTCAGAACAGCATCAGCTGGATGTCAACACTCCGTGGTTCAAGTATACAACAGAAAGACTTCGAGAAGTTTTCATCATGAATCATAACCAAGTTTTTCAGTATTTGAGCTCTCTTGAAACTCTTTTGTTCACATCTGATCTGGATCCACGCATTTTGAGCCTTTTCGATCATTTTAAAGCTTTAAGATCATAG

Transcript

ENSSYXT00000014074

TGCTAAATAAGCCTAACGGAGGAATTGTCATCTTTCTACCCCTTTGCTGGAATTTGCTTTTGACCGAAAAATGTCCAGGGAGAAAAGGAGATATCAAAGTGAAGATGAAGaAGGAAGAACACGGAAGCGAAGAAGAACAACAGAAGTTGTGGATATTGAAGACCGTCTAGAATCTCTTATCACACGTGTAGGAGAAAAGAGTACATCATCTCTTGAAAGTAATCTGGAAGGTCTTGCCAGTGTGCTGGAAGCTGATTTGCCTAATTACAAAGAACGCATCCTCAAGATTATTTGCACATGTGCTGCAAATCTACCAGAGAAAACAACTGTTTACAGCACACTAGTAGGACTTTTAAATGCAAAGAACTATGGATGTGGAGAGGAGTTTTTAGACATGATTCTGGAAAATCTCAAGGAAGTGCTGGTTGCTGCTCAGTTTGACAGAGCTAGATTGATGGTGCGGTTTCTTGCTGATCTGGTGAACTGTCGTGTTCTCATGCCTAGTGCACTTTTAGAGTTTTATGACAAGCTTCTGGCTGCTACCTTGGAGGAAAACATAACACAGGTTCGATCTGACTGGTTTGTGTACATGGTACTATCTTCGTTGCCCTGGGCTGGCAAGGAACTTTCAGAGAAAAAGGGTCAGGAATTTGAACAGCTGTTATCAACTATTGAGCACTATATAAGTCATAGACACAAGACTCACATTCCTTCGCTCCGAGTGTGGTCAAAAGATGAGCCTCACCCTCAAGAGGAGTATATGGACTGTCTGTGGGCACAAATCAAGAAACTGAAATCTGACAATTGGCAGGAAAAACATATCAGGAGACCTTATCTTGCATTTGATGATGTTCTTGGAGACGCTTTGCAGCATACCCTTCCATCATTCATGCTTCCAGTACTAAAGGATGGCATTGTATACCCTCTTCCAAAAGTAGTTTATAGAATGTTTGATTACACCGATGTACCTGAGGGTCCTTCCATGCCAGGAGCCCATGCAATTGAAAGATACTTAGTAGAGGAGGGTATTGAGAGAACAATACATGCACATTTTAAGGACAGAAAAGAATGTGCAAACCAGCTATTAAACTTGCCTGGAAAGTCTAAAGTACCAATGCATTACTGCATTATTGAGGTGATCTTTTCAGAGATGTTCAAACTTCCAAACTCACATCATCCCCAAATATTCTATGGCGCTTTAATTATTGAACTATGCAAATTACAACCAAATTCAATCCCTGGCATTGTTGCCCAAGCAACTGAACTGTTGTATGAGAGATTAAACTCAATGAACACAACTTGCGCTGAAAGGTTTGTCTACTGGTTGTCATATCACCTCAGCAACTTTCAGTTCAAATGGGGCTGGGACGAATGGGTTTCTGCCACTGATGATGGATTGGATTCACCTAAATGTACTTTCTTGAGTGAGCTGTTCGAAAGGATAAAAAGATTATCATACCATCAATTTCTGATTGAGAACATTCCTGAAGGATTGCATACCCTCCTTCCCGTTGCTCCTGCATCAAACTACAGATTCACAGAGGAACAAGGAGAGTTACCAGGAGCAGATGTCGCCAAAAACCTACTGGAAGCCATCAGAGCTAAGAAAGATGTAGATCAACTTCAGACCATTTTAAACAACATACCAGCAAATGCAACTGGTCGTGAGGACTTTAATACTGATGTGCCAGTGATCGACCACACTTTCCCACAATTAAGACTAGAGGTCTTGCTTCAGGTTGTGCTCAAACTTGGTTCCAAATCGTTCAGTCATTCTTTCAGTGCTCTAACGAGGTTCCACAAACTTCTTAAAAATGTCATTGTGAACGAAGAAAGTCAGATACATTGTCTGAAGATTGTGAATGAGTTTTGGTCCACAAATCCTCAGATGATGGTGGTGTTGGTAGATAAACTGGTACGCATGCAACTCACTGATTGCTCAGCAGTAATCAACTGGCTTTTTTCCAAGGACATGAAAGATAACTTCACAAAGTTATATGCGTGGGAAATAATGACAGGCACCTTAAAGAAAATGAGTAAACACACCAATAAGGTGTTGGGTGAAGTACAAGAAGCCAAAGAAAAGCTGACAAAACTGgaagaaaaagctaaaaaacAGCCTGGAGAAGCAAATGGTGATTCAAAACCTGACCCATGTCCAGAGGAAGAATTGGATAAAAAGCAGCAACAACTAGAAGAACTTACAGAAAAATTAGAAAATGCTCAGAGAACTCAAAAACAACTCTTCCTTATTGTTTTCCAGCGTTTCATCATGATCCTTACAGAACACATTGTGCGTTCAGAACAGCATCAGCTGGATGTCAACACTCCGTGGTTCAAGTATACAACAGAAAGACTTCGAGAAGTTTTCATCATGAATCATAACCAAGTTTTTCAGTATTTGAGCTCTCTTGAAACTCTTTTGTTCACATCTGATCTGGATCCACGCATTTTGAGCCTTTTCGATCATTTTAAAGCTTTAAGATCATAGGATTGAAGTTTCGAAGTTTTGAGGTTCCAAGGTCAGGGAGCAGATTAGGGTACAAGAAATATGTCGTGAAAGTCATTTTAAGATGGTTTAAATTATTTAAGAAACCAAGTTTCTCTTATTCTCAGACTATTGTCTCTCCGATCTTCTATTACAAACAGTCGTGTTGTTGACGGATTCTCTGTTCCTAATAGTTAGTCTTTCTCTGGATCCAATCATATAGTACAAcgttaatttttttcaagcgtTGTTATACAACTTAGCCTGACGAGTATCATTTTTTGTTCTGTTAAAGGCCATTTCTCATGTTGTATGACTTTTATAGTTGGGTGTTTAATTTGAGCTGTATATTTTTCTTGCAATGTTTGTCCAGTTCCGTGTACCCAGTGTCAAATAAATGATTTTCTTAACTGATCATTTTACCGCTGAAAATGAAAGTTTCCCTCTTATCGCGATGATTGCAAATGACAGCCAGATAACTTTTAAGAGAAGTTAGTTTTGTGGAATCTcgaattttttattgttattccCTGTAATCTTACTTCTAACCGCATGAATAGAGCAATTAGTTGCAACACCCTTATTGACACTTGTCGCTTTACCTGTAATCAGCGATGTGACGCAAGAGAATATGGCGTCTCACTTTTTGACATGCGTCGTTGACGTCTTCTAGTATGTTATCAATGTTTATATTCCACGTTCACATTCTATAGTAACATTTAACTCGTTGCAGTTAGAAATCTTTATATCCAATTTATATATTTTTGCTTGattcttattgttttagtaaagtTATTGTTGAAATGCACGTCGTGACCGTATTACGTGATCATTGTCGTCATCATCGTCATGCCTGTCTCGTCATTTGTGTCAGGATTGTTTCGTGCACTCAAAATTAGAGAGCGTAATAGCTCCTTACACAACCTTATCATAATAAGATACTGCTCCCAGAGACAATCTAAGCCCCGGGCTGTTGGCTTGCGTGCGAAAAATGACTCCCGC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6DIE2	Nuclear cap-binding protein subunit 1 OS=Xenopus tropicalis OX=8364 GN=ncbp1 PE=2 SV=1
Q6GQD0	Nuclear cap-binding protein subunit 1-B OS=Xenopus laevis OX=8355 GN=ncbp1-b PE=2 SV=1
Q5ZJZ6	Nuclear cap-binding protein subunit 1 OS=Gallus gallus OX=9031 GN=NCBP1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003730 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02854 all species →	MIF4G	MIF4G domain	Repeat	Interproscan
PF09088 all species →	MIF4G_like	MIF4G like	Repeat	Interproscan
PF09090 all species →	MIF4G_like_2	MIF4G like	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003890 all species →	Domain	MIF4G-like, type 3	Interproscan
IPR015172 all species →	Domain	MIF4G-like, type 1	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR015174 all species →	Domain	MIF4G-like, type 2	Interproscan
IPR027159 all species →	Family	Nuclear cap-binding protein subunit 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12412 all species →	CAP BINDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0016070 all species →	Biological Process	RNA metabolic process	Interproscan
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0000339 all species →	Molecular Function	RNA cap binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005845 all species →	Cellular Component	obsolete mRNA cap binding complex	Interproscan
GO:0005846 all species →	Cellular Component	nuclear cap binding complex	Interproscan
GO:0006406 all species →	Biological Process	mRNA export from nucleus	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
K12882	NCBP1, CBP80; nuclear cap-binding protein subunit 1	-	Spliceosome	ko03041	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 Micromussa lordhowensis 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 Micromussa lordhowensis, 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 →