Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Nuclear pore complex protein Nup98-Nup96.

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 g388 g388.t3 isoform g388.t3 3137879 3139243
chr_3 g388 g388.t3 exon g388.t3.exon1 3137879 3139243
chr_3 g388 g388.t3 cds g388.t3.CDS1 3137890 3139242
chr_3 g388 g388.t3 TSS g388.t3 NA NA
chr_3 g388 g388.t3 TTS g388.t3 NA NA

Sequences

>g388.t3 Gene=g388 Length=1365
ATTTTACAACAATGAATTTAGATGAAAATTTTAATTCTGATCCAACAAGTCCGTCAATAA
AGCTTGCAAAAGACATGCAAACAGATACACATAAATTGCAATTAATGAAAGCATCATTTT
TTGTTGAAGATGATGCTTTTTCAGTTATGAGTGATGCAACTGAAGGACGCGAGAGTCCAG
ATCAAATTGTTCCAACTGATTTTACTCCAAAACCATCGATTTTTGCAGTAACAGGATTAT
TGTCTAAACAATTTAAAATGTTTGATGATGCAGCCGCAGTTCAAGAATATGAGACAAGAG
ATTTTGAACAATCTAGCGAGCCTAAACGACAAGAATTAATTCAAACAATTTTCAAAGCAG
TTGGACCAAAATCACAGCCATTAATTGTTCGTCCTCGAGTAATGCTCTTTGATATTAGCG
ACATCAGTTTGCCAATGAGTGAGTCAATTTTGAATAACATGATACAGAAACCAAACAACA
CTGTTCCATTCTTTCACGGCAGAAAATTCAAAATTGGTTGGAGTCACGGTAATGAATTTA
CAGTTCTGCAAAGTCATGCGAGCAAGTCATTGTTTAAAGGACGTCTTCGTGATGATTTAT
CAAAATCATTTGTTAAATTAGCTCAAATCAAATCAATGTCACATAAAACCAATGCAAAAT
TTGACAAATCACTTGTTGAGCATTTAAAAATTCAATTGAAATATGATAAGAAAATTTCAA
TCAACGGATCTGACTGTAAATATTTTGAAGCTGATGGAAAGGCATTAGGACTGCATGAAC
ATTATGAATTGGCACAAAAATTGATAAAAGATTCACCCAATGAAAAGAATAGTTATGATG
CGACAGTCTGGTCTTTAATGGAATCTTTATGGGGGTGTATTGATAATATGAATATGGAAA
CACTCGATCATGGAACAATAATGCTACGAAGAGATCTTTTATCTCTTTGGCTGGAGAATG
TAGTTACTGATAACGATGTGTTTAAATCTAATCTTGATTATTTGGATCGATTAACAAATT
TAATGATGTGTCACAAAGTGAATGATGCATGTGACTTAGCGTTCGAAAATAACGATATAA
ATTTAAGTCTTTTGCTTTCACAAGCGAGTGGAAGTTCTTCAACTAGACAATTATTACAAC
ACCAGTTATCTTGTTGGCATGAAGTTGAAGCTGATGAGTTCATTGACGATAGAAGATTGA
AAATTCTTATGATGGTGAGCGGAATATCAGCGATGGAAGGAGCGAAAAAGTCCACTCTTA
ACATTTTTGAAAATCTAAATTGGTTAAAATGCTTAGCACTTCAAGTGTGGTATGTTTCAA
CATTAGTTTCTTCAGCAACTGATTCAATTTTGGCATATGTGAAAA

>g388.t3 Gene=g388 Length=451
MNLDENFNSDPTSPSIKLAKDMQTDTHKLQLMKASFFVEDDAFSVMSDATEGRESPDQIV
PTDFTPKPSIFAVTGLLSKQFKMFDDAAAVQEYETRDFEQSSEPKRQELIQTIFKAVGPK
SQPLIVRPRVMLFDISDISLPMSESILNNMIQKPNNTVPFFHGRKFKIGWSHGNEFTVLQ
SHASKSLFKGRLRDDLSKSFVKLAQIKSMSHKTNAKFDKSLVEHLKIQLKYDKKISINGS
DCKYFEADGKALGLHEHYELAQKLIKDSPNEKNSYDATVWSLMESLWGCIDNMNMETLDH
GTIMLRRDLLSLWLENVVTDNDVFKSNLDYLDRLTNLMMCHKVNDACDLAFENNDINLSL
LLSQASGSSSTRQLLQHQLSCWHEVEADEFIDDRRLKILMMVSGISAMEGAKKSTLNIFE
NLNWLKCLALQVWYVSTLVSSATDSILAYVK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g388.t3 Gene3D G3DSA:1.25.40.690 - 320 406 3.2e-06
2 g388.t3 PANTHER PTHR23198:SF17 NUCLEAR PORE COMPLEX PROTEIN NUP98-NUP96 17 449 0.0e+00
3 g388.t3 PANTHER PTHR23198 NUCLEOPORIN 17 449 0.0e+00
1 g388.t3 Pfam PF12110 Nuclear protein 96 333 450 0.0e+00

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.

Raw TPM values