Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Nuclear pore complex protein Nup93-1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g398 g398.t2 TSS g398.t2 3161215 3161215
chr_3 g398 g398.t2 isoform g398.t2 3161294 3161768
chr_3 g398 g398.t2 exon g398.t2.exon1 3161294 3161457
chr_3 g398 g398.t2 cds g398.t2.CDS1 3161294 3161457
chr_3 g398 g398.t2 exon g398.t2.exon2 3161520 3161700
chr_3 g398 g398.t2 cds g398.t2.CDS2 3161520 3161700
chr_3 g398 g398.t2 exon g398.t2.exon3 3161766 3161768
chr_3 g398 g398.t2 cds g398.t2.CDS3 3161766 3161768
chr_3 g398 g398.t2 TTS g398.t2 NA NA

Sequences

>g398.t2 Gene=g398 Length=348
ATGGATTTTACTACACTTATGCAGCAAGCGCAGAAGCTTGTAAATGAAACACAAAATAAT
GATGATCTACCGCGAGTTGAGCGTTCAATGCCGCAAATTTTAAAAGCAATAAATGAACTT
CATAGTAGAGTGACTTCATCCAGTAGTGCTCAAGATGTGCAAGCATATATTCTATTAGGA
TCAAAAGGTATTGATGTACCAAAGATTTCAAAAAATCTTGAAACTTTGAGCGCTCGAAAA
ACATTTGAGACATTAGATCCAGTTTATGACACAGATATTCATAGTTTTCTCAAAAATGAA
AAAGAAAATGCTATTCTATCAATTATTCAAGATGTTAACAAGAGTTCT

>g398.t2 Gene=g398 Length=116
MDFTTLMQQAQKLVNETQNNDDLPRVERSMPQILKAINELHSRVTSSSSAQDVQAYILLG
SKGIDVPKISKNLETLSARKTFETLDPVYDTDIHSFLKNEKENAILSIIQDVNKSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
g398.t2 PANTHER PTHR11225 NUCLEAR PORE COMPLEX PROTEIN NUP93 NUCLEOPORIN NUP93 DEAD EYE PROTEIN 2 115 0
g398.t2 PANTHER PTHR11225:SF4 NUCLEAR PORE COMPLEX PROTEIN NUP93 2 115 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005643 nuclear pore CC
GO:0017056 structural constituent of nuclear pore MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed