General information for g9068.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Regulator of nonsense transcripts 3B.
Parent gene
- The parent gene g9068 is located on chr_2: 35017674..35018427 (+ 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_2 | g9068 | g9068.t1 | TSS | g9068.t1 | 35017603 | 35017603 |
| chr_2 | g9068 | g9068.t1 | isoform | g9068.t1 | 35017674 | 35018427 |
| chr_2 | g9068 | g9068.t1 | exon | g9068.t1.exon1 | 35017674 | 35017928 |
| chr_2 | g9068 | g9068.t1 | cds | g9068.t1.CDS1 | 35017674 | 35017928 |
| chr_2 | g9068 | g9068.t1 | exon | g9068.t1.exon2 | 35017984 | 35018307 |
| chr_2 | g9068 | g9068.t1 | cds | g9068.t1.CDS2 | 35017984 | 35018307 |
| chr_2 | g9068 | g9068.t1 | exon | g9068.t1.exon3 | 35018380 | 35018427 |
| chr_2 | g9068 | g9068.t1 | cds | g9068.t1.CDS3 | 35018380 | 35018427 |
| chr_2 | g9068 | g9068.t1 | TTS | g9068.t1 | 35018477 | 35018477 |
Sequences
>g9068.t1 Gene=g9068 Length=627
ATGCCGGAAAAGGTTAAATCTAATGAATTAACGCCTGAAAAGGAAATTGTTAAACCAAAG
GCGATAAAGAAAGTAAAAACATTTCTAAATAAAGTTGTTATACGAAAATTACCACCAAAT
TTAACTAGCGAAGAATTTCTTGAAATAATTTCACCAATTCCGGATTATTCAGATTATTAT
TTTGTTAAAGCTGATTGGAGTTTAGGAGCAGAAGCTACTTCAAGAGCATATATTGAGTTT
AAGAACCAAGAAGATATATTTATTTTCAAAGATAAATTTGATGAATATGTGTTTGTGGAT
AATGTAAGAGGAACAGAATATCCTGCAATAGTTGAATTTGCACCATTTCAAAACTTGCCA
AAATCACGTGCTCGTAAAGACAAACATGTAAATTCGATTGAAAATGAACAACATTTCTTA
AATTTTCTTGAAATGCTTAAAAAATCAGAAGATGCTGAAAATCAAAAAGTTGAACCCAAG
CTCGAGTACAGTTATCAAATAAAGGATGACAAGAAAATTACATCAACTCCATTATTAGAA
TTTATTGCTGCATCAAAAGAAGAGAAACGAGAAGCAAAGAAAAAGAAAATTGAAGATAAA
AAGAAAGCACGAGAGGAAGAAAAGTAG
>g9068.t1 Gene=g9068 Length=208
MPEKVKSNELTPEKEIVKPKAIKKVKTFLNKVVIRKLPPNLTSEEFLEIISPIPDYSDYY
FVKADWSLGAEATSRAYIEFKNQEDIFIFKDKFDEYVFVDNVRGTEYPAIVEFAPFQNLP
KSRARKDKHVNSIENEQHFLNFLEMLKKSEDAENQKVEPKLEYSYQIKDDKKITSTPLLE
FIAASKEEKREAKKKKIEDKKKAREEEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9068.t1 | Coils | Coil | Coil | 182 | 207 | - |
| 5 | g9068.t1 | Gene3D | G3DSA:3.30.70.330 | - | 29 | 119 | 1.9E-33 |
| 4 | g9068.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 187 | 208 | - |
| 2 | g9068.t1 | PANTHER | PTHR13112 | UPF3 REGULATOR OF NONSENSE TRANSCRIPTS-LIKE PROTEIN | 25 | 204 | 6.1E-44 |
| 1 | g9068.t1 | Pfam | PF03467 | Smg-4/UPF3 family | 30 | 186 | 2.2E-45 |
| 3 | g9068.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 30 | 118 | 7.66E-27 |
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:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | BP |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14328 (regulator of nonsense transcripts 3)
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.
