General information for g13152.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear pore complex protein Nup205.
Parent gene
- The parent gene g13152 is located on chr_1: 28267090..28268312 (+ strand)
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_1 | g13152 | g13152.t2 | isoform | g13152.t2 | 28267090 | 28268312 |
| chr_1 | g13152 | g13152.t2 | exon | g13152.t2.exon1 | 28267090 | 28267829 |
| chr_1 | g13152 | g13152.t2 | cds | g13152.t2.CDS1 | 28267158 | 28267829 |
| chr_1 | g13152 | g13152.t2 | exon | g13152.t2.exon2 | 28267913 | 28267974 |
| chr_1 | g13152 | g13152.t2 | cds | g13152.t2.CDS2 | 28267913 | 28267936 |
| chr_1 | g13152 | g13152.t2 | exon | g13152.t2.exon3 | 28268031 | 28268312 |
| chr_1 | g13152 | g13152.t2 | TSS | g13152.t2 | NA | NA |
| chr_1 | g13152 | g13152.t2 | TTS | g13152.t2 | NA | NA |
Sequences
>g13152.t2 Gene=g13152 Length=1084
GTTTTGCTGCATCGTATGTTGGTGCAGAGCTTTTATTAGAAAATCGTGTCATTGGTATAC
TTTCACAAATGAAAGTTTTTGATTTACATCCTGATTTTCAAATAAGCAGCATGATGGACA
CTTCTGAGAATTCATTTATTCCTCCAATAAGTCATCGTTATCAACAACTTTTGTTTCCTG
CATTAAGTCTTTGTGATGTCATTTTAATCACTCTCGGACCAGAGAATCAATCAGTGATTA
CTCAAATTACACACTTTTTATTATCGCATTCTGATATCGTTGAAATAGTGCTACGAGCTG
GAACACCATCTATATCATTAGGTCTTTTAAAAGAATTATCAGGATTAACAGGGCTTATTG
CGCGTGCTTCAAATCAAAGTATCAGCGAATTAATGGATCCTAGTGGAAACCATGATATCG
GTGCACATTTATATCGTCTACAAAAATTAATGATGGCTCTATTTCCACGTTTTACTCTCA
CTAATCCTAATTTAAAAGAAGCTCAAAGAATTTTCGGAAACATGCAGGCAGAAAATGAAG
AAACTGAAAAACAAAGAGCAGAAAGAACTTTGACTTTCCTTCAAGTAGCAGCAAACATTT
CACTCTATGCTAGAAATTGTATTGCTAATCATTCTGTAGATCATCGAACAACAAAAGTTT
TATTTTCAATCAATACTGAGACAATTTCAAGTGGCCATGAATCAGCAACTGCAACATCTT
CACCTGATTTAAGTATCGTTACCAACAATAAGCTTGGATGTTAATATTGCACAACAGCAA
CAGCATTTAAGTGATAAACTTGTTATTGTGGTCACACTTGGATTACTATATGTTGCGTGC
CATAACACCTGCTCTTCAATTAAATGGTTTCTCATATGGCATAGGAAACGATGTGACGCC
AGAAGTGAGAACAATGAGAATAACAAATGAAGAAATTGCCAAACTGAAACATAATCTAGT
GACTGTGTTTAGTGAAACATTTTCAAAGCAACTATTAAGCACTCAAGAGACGCAAACATC
AAATTTCATTGACGTCCTTTTGAGACGAATTAAACGTTTAATTCAATTTGTTCCCGTTGA
TTAA
>g13152.t2 Gene=g13152 Length=231
MKVFDLHPDFQISSMMDTSENSFIPPISHRYQQLLFPALSLCDVILITLGPENQSVITQI
THFLLSHSDIVEIVLRAGTPSISLGLLKELSGLTGLIARASNQSISELMDPSGNHDIGAH
LYRLQKLMMALFPRFTLTNPNLKEAQRIFGNMQAENEETEKQRAERTLTFLQVAANISLY
ARNCIANHSVDHRTTKVLFSINTETISSGHESATATSSPDLSIVTNNKLGC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g13152.t2 | Coils | Coil | Coil | 142 | 174 | - |
| 1 | g13152.t2 | Pfam | PF11894 | Nuclear pore complex scaffold, nucleoporins 186/192/205 | 1 | 100 | 1.2E-21 |
| 2 | g13152.t2 | SUPERFAMILY | SSF53613 | Ribokinase-like | 52 | 168 | 4.38E-5 |
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 |
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.
