General information for g10202.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear pore glycoprotein p62.
Parent gene
- The parent gene g10202 is located on chr_1: 8201237..8202665 (+ 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 | g10202 | g10202.t12 | TSS | g10202.t12 | 8200328 | 8200328 |
| chr_1 | g10202 | g10202.t12 | isoform | g10202.t12 | 8200466 | 8201237 |
| chr_1 | g10202 | g10202.t12 | exon | g10202.t12.exon1 | 8200466 | 8200483 |
| chr_1 | g10202 | g10202.t12 | exon | g10202.t12.exon2 | 8200551 | 8201237 |
| chr_1 | g10202 | g10202.t12 | cds | g10202.t12.CDS1 | 8200554 | 8201237 |
| chr_1 | g10202 | g10202.t12 | TTS | g10202.t12 | 8201338 | 8201338 |
Sequences
>g10202.t12 Gene=g10202 Length=705
GGGTGTTAAATAAAGTGAAATATGGCATCGACTGGATTTTCGTTAACTTCAGCTCCTACT
CAACCAGCTGCAACAACTACACAAATAAGTTTAACTACAAATACCTTAACTACTCCATCT
TCATCAGCACCGGCAAATTCGATGAATTTTTATAGTTTAGAAGAATTGATTAATAAGTAC
AACCTTGAATTAGCTGAACAAGAAAAGATTTTTATTAATCAAGCTACACAAGTAAATGCA
TGGGATAATATTTTACTAAAAAATGGAGAAAAAATAGTTGAATTGAATAAGGCAGTGGAA
AAAGTCAAGGCAGATCAATCAGCGATGGAACAAGAATTAGAATTCATAACTGCACAACAA
GCTGAATTATTAGAATCTATAATTCCTCTTGAGCAAGAATTGGCCAAAATTCCTCAACAA
ATCGATGTAGATCGCTCACAAACCTATTTAATGGCAGAAACTCTTGATTCTCAACTGAAA
CAAATGTCTGAGGATTTAAAAGAAGTTATTGAACATTTGAACGAAGCAAACAAATTCGCT
GATCCGAGTGATCCAATGGTTCAAATTGGAAAAATTCTTAATGCTCATTTTACATCACTT
CAATGGATAGAAGACAAAACTCAAGCCATTAATAATAAATTAGAAGAAATTTCAAAAATG
AGTTCTCTTTATCAGAAGGATCGCTCATTTCGTTATGACATTTAA
>g10202.t12 Gene=g10202 Length=227
MASTGFSLTSAPTQPAATTTQISLTTNTLTTPSSSAPANSMNFYSLEELINKYNLELAEQ
EKIFINQATQVNAWDNILLKNGEKIVELNKAVEKVKADQSAMEQELEFITAQQAELLESI
IPLEQELAKIPQQIDVDRSQTYLMAETLDSQLKQMSEDLKEVIEHLNEANKFADPSDPMV
QIGKILNAHFTSLQWIEDKTQAINNKLEEISKMSSLYQKDRSFRYDI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10202.t12 | Coils | Coil | Coil | 85 | 112 | - |
| 6 | g10202.t12 | Coils | Coil | Coil | 145 | 165 | - |
| 5 | g10202.t12 | Gene3D | G3DSA:1.20.5.170 | - | 72 | 134 | 3.0E-21 |
| 2 | g10202.t12 | PANTHER | PTHR12084:SF0 | NUCLEOPORIN 62-LIKE | 6 | 212 | 8.2E-67 |
| 3 | g10202.t12 | PANTHER | PTHR12084 | NUCLEAR PORE GLYCOPROTEIN P62-RELATED | 6 | 212 | 8.2E-67 |
| 1 | g10202.t12 | Pfam | PF05064 | Nsp1-like C-terminal region | 31 | 135 | 7.4E-30 |
| 4 | g10202.t12 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 17 | - |
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 transcript has been annotated with K14306 (nuclear pore complex protein Nup62)
Pathway
- This transcript belongs to the following pathways
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