Gene detail

Detailed information of gene04685.t1 in Actinoscyphia liui

Genomic Location: chr2:9580385...9609260
NR annotation: XP_020893315.1, nucleoporin p54 [Exaiptasia diaphana]
Species Actinoscyphia liui · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

gene04685.t1

CTGATTTGGTCGATTTATGGTCGATTTGGTCACTGATTTGACAAAACATAGAATGATAATAATAGTTTTATTGTTGGAATGACTACTGCATTTACGTTTGGGACGCCAAAGACAGGCACTTCTGCGTTTGGTACAGCTACTACAACTAGTGGTTTCTCGTTTGGTACTCCATCTACGTCCACTTCTACTGGAACAGCAGCATTATTTGGCGCGTCTGCTCCAACCACAAGCTCGTTTACTTTTGGCTCTGGATTAGCAACTGGTTCAGCATTCGGTGCCAAAACTGCTCCTGCTACTACTTTTGGAACTGCAAGTACGTTTGGCAGTAATGCACCATCCTTTGGCAGTTCTTTTGGTACGGGACTGGGTACTAGTTCCTTTGGAGTGCCTGCAGTAGGGACTGGGACTACTGTGGGGTTTGGCCAACAAGCAACATCTTCTGGACTGGCACAAAATATTTCACCAATGGTTCTTATGAACTTGTGTTTATCCAACCCACCGATACATGGTGATGAAAGAGATGGTATTATTGCTAAACTAAACCAGGTGCAGGCATACTGGGGCACAGGAAAGGGCTACTACAATCAGCAGGGCAATGCTGTTGCATTTACACCTGAAAATCCATATTGTAGATTCAAGGTTGTGGGCTATAGTAGATTACCAACAGCTAGTAATGATGATGGATTTGTAGGGATTCAAATCAAAAAGAAAGAGTCTGAGGTTTATCAACAACAACAAAATTTAGTGAGTGAGCTACAGAAATGTTTTGGTAATAAACCCACTATCATGGTGTGTGTTGATGGACTGAAACCTCTCCCTGACGACAGTACTGAAGTAGTCTTCAAAGTAGTTGAACGTGCTGATAATGGTATGACCAAAACATTCCCTGCTAACGAAGTCTATACCTTTCTAATCCAAGGCAATGTTAAAACTCAACTACAAAACATGGGAGTTACTAATATAACAGCCAAAACAAACATGCCACTTGCTCTGCTGCAGCAGTATCTAAACACACCTCCTGCAGGTATTGATTCCTTGTTATGGGAGCAAGCCAAGAAAGACAATCCTGACCCTCAAAAGTTGATCCCAGTACCTATAACTGGCTTTGATGAACTAAAAAAACGACTTGAATTTGAAGACCAAGAAACAGCACAACACCAAAAACGACTATCAATGATGAGTGAAGAGATTGCAGCACTGCAGTGTAACCATGCCACAACCATGGCAAAGCTTGCACAGTTTAAACGAAAGCATTTAGAGCTGAGTCACAGAGTACTTGAGGTCATGGTAAAACAAGAATCAATACGTAAAGCTGGGTATTCAGTACAAGCTGAAGAAGAACATCTCAGGGTGCACTTAGAATCCTTGCAAGCAGAACTCAATGCCCCTCTACAGTTTAAGGCCCGTCTAAACGAATTGTTATCTCAAATTCGACTACAACAAAGCCAGGGTGTTGGCAGTAAGGACAAGGCTGAAGGCCGATACACTATGGATCCCTCGCTACAGAACGAGCTCAAGCAGCATCTCGAACAGCAACAAGAAGGCTTAATGCATCTCATCAGCATCATTAAAGATGATATCGAGGATCTAAAGACCATTGATCAAGGGCTTGGAGAGAGTTTAGTAGTACGATAACCAACTCAACACTGGACTTTTCTATTCGCAATCGACACAACATGAATATTTGAACGGGACAAGTACAGAAATGGAGTAAAGAGATGCATGGGTGCGGTCACAACACTAGATGGTGCACAGTATAAGTTTGCATATATTTTATGTACTTGTAATAACGCTAAGACTATAGCTACTGGTATTCACTACCATACAGTCTTCATTACAGTAGGTCTTGTATGACCATACCGTGCTGTATGGTTTGTCATAATCTGCTAATAGTGATTGTTTGATGTGTGTGGGTTAGAACACAGGTCATACCAGCGTACGTACACAGTGGTCAACTGATAATTGTATTGACAAGGAGTTAATGAGTATATATGGTCAGTTGTACGAATATTTATTTCATTACATTGCTGACACTCGCCTTACAACCACTTGCCATGCCAAACCTTTACTTAGTGGTAAAAAAACACAGCTATCATTCAATTGACATTCGGTAAAGACTGGTTTAGCAATGTTTGACCACCATGTCTAAACAATCATGACACTTGCTGGCTAGAAACATCCCACGAGTATTTCACGTCAACAACTCTACTTTGTCTGGTTTTTGTGGTGTCTACAGCTGGGTCTTAATCACCAACAATAAATAATGCATGTTACTACACACGAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7Z3B4	Nucleoporin p54 OS=Homo sapiens OX=9606 GN=NUP54 PE=1 SV=2
P70582	Nuclear pore complex protein Nup54 OS=Rattus norvegicus OX=10116 GN=Nup54 PE=1 SV=1
Q8BTS4	Nuclear pore complex protein Nup54 OS=Mus musculus OX=10090 GN=Nup54 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005802 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13874 all species →	Nup54	Nucleoporin complex subunit 54	Domain	Interproscan
PF18437 all species →	Nup54_C	Nup54 C-terminal interacting domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR024864 all species →	Family	Nucleoporin Nup54/Nup57/Nup44	Interproscan
IPR025712 all species →	Domain	Nucleoporin Nup54, alpha-helical domain	Interproscan
IPR040985 all species →	Domain	Nup54, C-terminal interacting domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13000 all species →	NUCLEOPORIN P54	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005643 all species →	Cellular Component	nuclear pore	Interproscan
GO:0006607 all species →	Biological Process	NLS-bearing protein import into nucleus	Interproscan
GO:0006999 all species →	Biological Process	nuclear pore organization	Interproscan
GO:0017056 all species →	Molecular Function	structural constituent of nuclear pore	Interproscan
GO:0036228 all species →	Biological Process	protein localization to nuclear inner membrane	Interproscan
GO:0044613 all species →	Cellular Component	nuclear pore central transport channel	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 gene04685.t1.

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 Actinoscyphia liui 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 Actinoscyphia liui, 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 →