General information for g13195.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear pore complex protein Nup160-like protein.
Parent gene
- The parent gene g13195 is located on chr_1: 28455021..28458773 (+ 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 | g13195 | g13195.t2 | TSS | g13195.t2 | 28450619 | 28450619 |
| chr_1 | g13195 | g13195.t2 | isoform | g13195.t2 | 28450813 | 28451743 |
| chr_1 | g13195 | g13195.t2 | exon | g13195.t2.exon1 | 28450813 | 28451656 |
| chr_1 | g13195 | g13195.t2 | cds | g13195.t2.CDS1 | 28450813 | 28451656 |
| chr_1 | g13195 | g13195.t2 | exon | g13195.t2.exon2 | 28451723 | 28451743 |
| chr_1 | g13195 | g13195.t2 | cds | g13195.t2.CDS2 | 28451723 | 28451727 |
| chr_1 | g13195 | g13195.t2 | TTS | g13195.t2 | NA | NA |
Sequences
>g13195.t2 Gene=g13195 Length=865
ATGAAATTTCGTGAAGTTGCACCGAATTCGGCTTCTGAAGAATGGAAAGATATCAAATTG
AACATTGGAGGTAGCCATAGCACTCTACAAGACATTAAAGTACAAAGGCAAGCTGCAGGT
TTTTGCTACAAGAATGATGAATTTATAAGAAATCGATTTATTTACTGGCGTACTTGTGAT
GATATTGTGCTAGAATTAAGTGAAAATAGTCTGGATGTCAATTTAAAGAACAAGAATTTA
CGATTAACATTTGAAGAGTCCCCAATTTTAGCAGTAAATATCAGTGAAACTCATGACAAT
GTCGTGATTCTTGTTACTACAATCAGCAACATTCATCGATTTCAATTTATTCATCCAAGA
AGAAATATTGGATCAAATGGCGAGCAAAATGAAAATTCAATCTTCAATTCTATTTCACAA
GAGTCAGTAAAAGATCCTTCATCGTTTTATACAATTAGCAATTTGCTCGCTCAAAATGTT
CCTCATTCAGCTGCTTGCTACTTATCACCAACAAGTGAAGATGCGTATTTTGCAGTTGCT
CATACAAATCATCTCTTACTCTTTCAAATGAATTGTTTTAGTGGACATACTGGTGTTATT
GAATTGAAAAACTTTCAAATACTTCCTAAAATTTTTAGCAACTTTACAGATGCTATTCGT
GGTAAAAGTAATGTGAATGATAGTAACTATGTAACATCGATGGTATTTGATACTATTGGT
GGTGAAAATGTTCTTTATGCACTATATCGGGATAATAACATTCGAATGTGGTCAACAAGA
ACTGGTCAATGTTTATTTACAATGAATATTGTTAGAGATAACGACGAAAGAAGAAGTCAA
GGAAAATAACATTCTGAAAAAGTCA
>g13195.t2 Gene=g13195 Length=282
MKFREVAPNSASEEWKDIKLNIGGSHSTLQDIKVQRQAAGFCYKNDEFIRNRFIYWRTCD
DIVLELSENSLDVNLKNKNLRLTFEESPILAVNISETHDNVVILVTTISNIHRFQFIHPR
RNIGSNGEQNENSIFNSISQESVKDPSSFYTISNLLAQNVPHSAACYLSPTSEDAYFAVA
HTNHLLLFQMNCFSGHTGVIELKNFQILPKIFSNFTDAIRGKSNVNDSNYVTSMVFDTIG
GENVLYALYRDNNIRMWSTRTGQCLFTMNIVRDNDERRSQGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g13195.t2 | PANTHER | PTHR21286 | NUCLEAR PORE COMPLEX PROTEIN NUP160 | 7 | 276 | 0.0e+00 |
| 1 | g13195.t2 | Pfam | PF11715 | Nucleoporin Nup120/160 | 45 | 275 | 0.0e+00 |
| 3 | g13195.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 164 | 274 | 6.8e-06 |
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:0005515 | protein binding | 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