Gene detail

Detailed information of FUN_025097-T1 in Acropora pulchra

Genomic Location: ptg000018l:13751115...13794945
NR annotation: XP_015766188.1, PREDICTED: nuclear RNA export factor 1-like isoform X2 [Acropora digitifera]
Species Acropora pulchra · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

FUN_025097-T1

ATGTCAAAAAATTTGTTCGCCAAAGCCGTTGAAGATGCAACGTTCACAGTGACTAAGTCTCCAGATGGATCACGGAGCTTCAGAGCTGAAGATAGACCAACTAGGGGAAGATCTCATCGTGGCTACTCGAGGGGAAGAGGGAGAGGACGTGGTCGTGGTAACTATCGAACCAGAGGCAGCTTTCCTCATCCAAGGTCACACCTAGGTGATGATGATGATGATGATGATATCCGCATGTATTCAATGGATGAAGGCCTGAGATCGGATTCAAGATTTAATCCTTATCGATCAAGACCTCCATCTCGTCGTGGCGGAAGAGAGGGAAATAACAACAGAGGTGATATTAAGTCCAGATTAGGGGCAGCTCCCTTTAACAAAGGAAGCAGTGGTCAAGACTGGTTCAAAGTTGTGATCATAGAAGGCCAGAAACACGACAAAGAGTGGTTAATAAGAAAACTGCAGAATACATGTGAAGAAGCCTTTCAACCCATTGATTTTCACATCATGAAAGGAGACAGTGTAGCATTTTTTGTGGAAGGAAGTAAAGCTGCAGAAGCTTTGAAGAAAGTGAGCCATAAGATTACAGTAAGAGATGGCTCAAAGCTCATATTCACTGTTCGGTCCAGTGGCGCACCTCATAATCCAAACAGTGTATTTACTACGGCTGTGGATGGTTGCCGTGGCAATACCAGGGAAGGCAACAATACTCCAGATGACAACACCAAAGAAATTTTAAAGCATTGCTTGGGTAAGCGTTATGATGTAATGTCAAAGGCTCTCAATCTCTCAGACCTTTTCCATGATGAAGTGCTGAATGAACATAATGTGCAAGGAGCATTATCAAAGCCTTGGTTAGCTTCAAGGATTGTGCAGATCATTGGTGAGAACTGTCCAGAGGTTTTATCACTGGATCTAAGTAACAACAAACTGAGAAACTTAGATGGCTTCAAGGACCTTGGACAACAAGCATCAAATCTAAAACATCTCAAAGTGTGTAACAATCAGCTCAGGGCTGTTGAGGACCTTGACAAGATAAAATCGTTGAGTCAGCTCACCTCCTTGGAGCTTGATGGAAATCCTCTTTGTGACATGTTTCAAAATAAAGGAAGTAATTACATCAACTCTGTAAGAAGCAGGCTTCCAAAAATCACCTTATTGGATGGTCATGAACTTCCTCCGCCAATTGGCTTTGATCTTCCCTCTCAACAAGCATTGCCTCCATCAAAGGACAGTTTCTTTTGTGATCCTCAAATACAAACGCTGGTTTTGAAATTTCTTGAACAGTATTTTAAGATCTATGATACAGAGGATAGGCAAGACTTGCTTGACGCTTATCATGACCAGGCCATATTCTCAATGTGCTTGCATTTTGGAACAATGAGCAAGGACCGTAGTGCTCCAAGGGGTCCTTCTCTTGGAGAGTACTTGAAAAACAGTAGAAACATGATGCGAGTCACAGAACCAGAACGACGTGTTGGTCTCTTGAAGCACTCAAGGCTGTCCGTGGTTGCGTTTTTGAATGAGCTTCCTGCCACCAAACATGACTGGTCCAGTTTTAAAGTTGATGTGAGCCTTGCTTTGCCAACTTGTCTGTCATTTGCTGTGCGGGGTTTGTTCATGGAGAATTCCAAAACCCTGCGTTCGTTTTCAAGAGTGTTTCTTGCTGTTCCTGGTTCTGGTGGAAAAGCGTTGAGCATCATTAACGATGAACTTCACGTCCGAAATGCCTCACCAGCTCAAGTTGAGCGTTTTGCTAATGAAACATCTGCGTCCAGCACAGAGAAGGTCAGCGCAGAAGTGTTCCCTGTGTCATGTACACCTCAGCAACAAGAGATGCTTCTGAAGTTTTCACAACAATCGACAATGAATTTGGAGTGGTCATTCAAATGTCTCAAGGAAAATAATTGGGACTATGGAAAAGCTGCTCATGCCTTTACTTCACTAAAGAACAATGGCAGTATACCTCCTCAAGCATTTATCAAGTCAAGCTAG

Transcript

FUN_025097-T1

TTCGCCCATAGCATGTCAAAAAATTTGTTCGCCAAAGCCGTTGAAGATGCAACGTTCACAGTGACTAAGTCTCCAGATGGATCACGGAGCTTCAGAGCTGAAGATAGACCAACTAGGGGAAGATCTCATCGTGGCTACTCGAGGGGAAGAGGGAGAGGACGTGGTCGTGGTAACTATCGAACCAGAGGCAGCTTTCCTCATCCAAGGTCACACCTAGGTGATGATGATGATGATGATGATATCCGCATGTATTCAATGGATGAAGGCCTGAGATCGGATTCAAGATTTAATCCTTATCGATCAAGACCTCCATCTCGTCGTGGCGGAAGAGAGGGAAATAACAACAGAGGTGATATTAAGTCCAGATTAGGGGCAGCTCCCTTTAACAAAGGAAGCAGTGGTCAAGACTGGTTCAAAGTTGTGATCATAGAAGGCCAGAAACACGACAAAGAGTGGTTAATAAGAAAACTGCAGAATACATGTGAAGAAGCCTTTCAACCCATTGATTTTCACATCATGAAAGGAGACAGTGTAGCATTTTTTGTGGAAGGAAGTAAAGCTGCAGAAGCTTTGAAGAAAGTGAGCCATAAGATTACAGTAAGAGATGGCTCAAAGCTCATATTCACTGTTCGGTCCAGTGGCGCACCTCATAATCCAAACAGTGTATTTACTACGGCTGTGGATGGTTGCCGTGGCAATACCAGGGAAGGCAACAATACTCCAGATGACAACACCAAAGAAATTTTAAAGCATTGCTTGGGTAAGCGTTATGATGTAATGTCAAAGGCTCTCAATCTCTCAGACCTTTTCCATGATGAAGTGCTGAATGAACATAATGTGCAAGGAGCATTATCAAAGCCTTGGTTAGCTTCAAGGATTGTGCAGATCATTGGTGAGAACTGTCCAGAGGTTTTATCACTGGATCTAAGTAACAACAAACTGAGAAACTTAGATGGCTTCAAGGACCTTGGACAACAAGCATCAAATCTAAAACATCTCAAAGTGTGTAACAATCAGCTCAGGGCTGTTGAGGACCTTGACAAGATAAAATCGTTGAGTCAGCTCACCTCCTTGGAGCTTGATGGAAATCCTCTTTGTGACATGTTTCAAAATAAAGGAAGTAATTACATCAACTCTGTAAGAAGCAGGCTTCCAAAAATCACCTTATTGGATGGTCATGAACTTCCTCCGCCAATTGGCTTTGATCTTCCCTCTCAACAAGCATTGCCTCCATCAAAGGACAGTTTCTTTTGTGATCCTCAAATACAAACGCTGGTTTTGAAATTTCTTGAACAGTATTTTAAGATCTATGATACAGAGGATAGGCAAGACTTGCTTGACGCTTATCATGACCAGGCCATATTCTCAATGTGCTTGCATTTTGGAACAATGAGCAAGGACCGTAGTGCTCCAAGGGGTCCTTCTCTTGGAGAGTACTTGAAAAACAGTAGAAACATGATGCGAGTCACAGAACCAGAACGACGTGTTGGTCTCTTGAAGCACTCAAGGCTGTCCGTGGTTGCGTTTTTGAATGAGCTTCCTGCCACCAAACATGACTGGTCCAGTTTTAAAGTTGATGTGAGCCTTGCTTTGCCAACTTGTCTGTCATTTGCTGTGCGGGGTTTGTTCATGGAGAATTCCAAAACCCTGCGTTCGTTTTCAAGAGTGTTTCTTGCTGTTCCTGGTTCTGGTGGAAAAGCGTTGAGCATCATTAACGATGAACTTCACGTCCGAAATGCCTCACCAGCTCAAGTTGAGCGTTTTGCTAATGAAACATCTGCGTCCAGCACAGAGAAGGTCAGCGCAGAAGTGTTCCCTGTGTCATGTACACCTCAGCAACAAGAGATGCTTCTGAAGTTTTCACAACAATCGACAATGAATTTGGAGTGGTCATTCAAATGTCTCAAGGAAAATAATTGGGACTATGGAAAAGCTGCTCATGCCTTTACTTCACTAAAGAACAATGGCAGTATACCTCCTCAAGCATTTATCAAGTCAAGCTAGCCGTGTGTTCCCTTCCTTGGTGTCCAAGTTTTATTTCATACTTTAAAGGAGAACAAGTTGTACCAACATTTTAACGTAATTTTAACTCACAATAACGATTTACAGTGATGTTCGTCAAGCAAATGTGTTGGTGTCTGTCATCTGTTATAATTTTAAAAGAGATGTGTTATATTGAGAAAGTTATTAAAGTTTATTCAATCGTAGACTTTTTAAGCGATTATCTTACTAAGTGCAGACCTGTATGAATTAGTTATCCTTACAATTCAGTGGGCCTCAGATAATGGTTATATGAGCATCCAATTCATCTTTTTAATACTTTATAATGTTACTGAATTCCTCACAAGAACAAAATCGACTTGAAGTCAACGACTGCATTCACGTAAACTCTCTTTTCATTTTGTGACCTTAGATTTGCATCTTGCTCAGTTCAACGCTGTACGTCTAAGCGACAAAATTTAGAATTAGGCAATTTTACAATAGTCAAATTTCCACTGTGAAGACGTAACAAAATTGGCTGTACCAGAACCAGGAACAACTTTCCCATACATTTATTGGTATCGACTAGTAAACCGGAAATAATACAAACCCATACTAAACTTAACACTGTAATCAACGCTTTAGAAACTTAAGATCGAACTCGCTATATATTCGACACGGGAAAGAAAACATGCAACATCAGAATAAATTACCTCTATCGATATAACTGGAACTTAATTAAACCTACAAACCAATTAAAAACAACTAAGGCAAGAAACATAACCAAATCAATCTCACATCGATCTAAATAAATGATTTACAACTAACTTAAGAGAGTGCCATGAAACTAACATACAGAAAAACCAAAGAGAGGGAATACTCGCATATCAGTTCTGCTACGCCGATGGCTTGAAAAGATGGAAAACCAAAAACAGAATACAACTAGCACACAATTACACATGCTGACAACGACTAATAAAAAGGGCACGTG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9UBU9	Nuclear RNA export factor 1 OS=Homo sapiens OX=9606 GN=NXF1 PE=1 SV=1
P58797	Nuclear RNA export factor 1 OS=Coturnix japonica OX=93934 GN=NXF1 PE=1 SV=1
Q5R752	Nuclear RNA export factor 1 OS=Pongo abelii OX=9601 GN=NXF1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003681 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09162 all species →	Tap-RNA_bind	Tap, RNA-binding	Domain	Interproscan
PF03943 all species →	TAP_C	TAP C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009060 all species →	Homologous_superfamily	UBA-like superfamily	Interproscan
IPR005637 all species →	Domain	TAP C-terminal (TAP-C) domain	Interproscan
IPR015245 all species →	Domain	Nuclear RNA export factor Tap, RNA-binding domain	Interproscan
IPR030217 all species →	Family	Nuclear RNA export factor	Interproscan
IPR001611 all species →	Repeat	Leucine-rich repeat	Interproscan
IPR032710 all species →	Homologous_superfamily	NTF2-like domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR032675 all species →	Homologous_superfamily	Leucine-rich repeat domain superfamily	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR018222 all species →	Domain	Nuclear transport factor 2, eukaryote	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10662 all species →	NUCLEAR RNA EXPORT FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0051028 all species →	Biological Process	mRNA transport	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006406 all species →	Biological Process	mRNA export from nucleus	Interproscan
GO:0016973 all species →	Biological Process	poly(A)+ mRNA export from nucleus	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	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
K14284	NXF, TAP, MEX67; nuclear RNA export factor	-	Ribosome biogenesis	ko03009	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 Acropora pulchra 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 Acropora pulchra, 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 →