General information for g13055.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Regulator of nonsense transcripts 2.
Parent gene
- The parent gene g13055 is located on chr_1: 27676292..27678890 (- 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 | g13055 | g13055.t2 | TTS | g13055.t2 | 27675859 | 27675859 |
| chr_1 | g13055 | g13055.t2 | isoform | g13055.t2 | 27676292 | 27676828 |
| chr_1 | g13055 | g13055.t2 | exon | g13055.t2.exon1 | 27676292 | 27676828 |
| chr_1 | g13055 | g13055.t2 | cds | g13055.t2.CDS1 | 27676293 | 27676799 |
| chr_1 | g13055 | g13055.t2 | TSS | g13055.t2 | NA | NA |
Sequences
>g13055.t2 Gene=g13055 Length=537
TAAAGCAAAAGATAAGAACACCTATTCAGATGTATATTAGATATCTCATATTTGAGGAGC
TACATAAAGGAAATGTTGAAAAGATTGTTAAATATTTGAGAAAATTGAATTGGGATGATT
CAGAAGTGAGCGATTATGTGATTAAATGCTTAACAAAAGCTTATACATTTAGATGGCATT
TAATTCGTTCCTTAGCTGATGTTGTCAGTGCATTGAGCTCTTATCAAGAGAAAGCTGTCA
CTAGAGTTATTGATGGTGTTTTTGAAGATATTCGAGCTGGATTAGAAATTCATTCACCAA
AACTTGCACAAAGAAGAATAGCAATGGCAAAATATTTAGGTGAACTATATATCTATCGAC
TTGTCGATTCACAGAACGTGTTCAACACTCTTTATAGCATCATTTCATATGGTGTAACTT
GGAATCATGAAATATTCTCACCAGTTGATCCACCCGAATCAATGTTTCGACTAAAATTAG
CTTGTACTATGCTTGATACATGTGGTGCATATTTTCAAAGTTTATCGAGCAAGAAAA
>g13055.t2 Gene=g13055 Length=169
MYIRYLIFEELHKGNVEKIVKYLRKLNWDDSEVSDYVIKCLTKAYTFRWHLIRSLADVVS
ALSSYQEKAVTRVIDGVFEDIRAGLEIHSPKLAQRRIAMAKYLGELYIYRLVDSQNVFNT
LYSIISYGVTWNHEIFSPVDPPESMFRLKLACTMLDTCGAYFQSLSSKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13055.t2 | Gene3D | G3DSA:1.25.40.180 | - | 1 | 169 | 0e+00 |
| 2 | g13055.t2 | PANTHER | PTHR12839 | NONSENSE-MEDIATED MRNA DECAY PROTEIN 2 UP-FRAMESHIFT SUPPRESSOR 2 | 2 | 169 | 0e+00 |
| 3 | g13055.t2 | PANTHER | PTHR12839:SF7 | REGULATOR OF NONSENSE TRANSCRIPTS 2 | 2 | 169 | 0e+00 |
| 1 | g13055.t2 | Pfam | PF02854 | MIF4G domain | 4 | 163 | 0e+00 |
| 5 | g13055.t2 | SMART | SM00543 | if4_15 | 1 | 169 | 1e-07 |
| 4 | g13055.t2 | SUPERFAMILY | SSF48371 | ARM repeat | 2 | 169 | 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:0003723 | RNA binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | BP |
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.
