General information for g3586.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Regulator of nonsense transcripts 1-like protein.
Parent gene
- The parent gene g3586 is located on chr_3: 26561743..26562755 (+ 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_3 | g3586 | g3586.t12 | isoform | g3586.t12 | 26560433 | 26561243 |
| chr_3 | g3586 | g3586.t12 | exon | g3586.t12.exon1 | 26560433 | 26560503 |
| chr_3 | g3586 | g3586.t12 | exon | g3586.t12.exon2 | 26560567 | 26560704 |
| chr_3 | g3586 | g3586.t12 | cds | g3586.t12.CDS1 | 26560620 | 26560704 |
| chr_3 | g3586 | g3586.t12 | exon | g3586.t12.exon3 | 26560764 | 26561243 |
| chr_3 | g3586 | g3586.t12 | cds | g3586.t12.CDS2 | 26560764 | 26561242 |
| chr_3 | g3586 | g3586.t12 | TSS | g3586.t12 | NA | NA |
| chr_3 | g3586 | g3586.t12 | TTS | g3586.t12 | NA | NA |
Sequences
>g3586.t12 Gene=g3586 Length=689
TCTAAAAAAGCAAGCAGAAAAGGAATTATTAGATGCTGCTGATGTCATTTGTTGTACATG
TGTTGGAGCAGGAGATCCACGTCTATCTCGCATAAAGTTCAATTCAATTTTAATTGATGA
GTCAATGCAGAGCACTGAGCCTGAAGCCATGGTTCCAGTCGTTTTGGGCGCACGTCAATT
GATTCTTGTTGGAGATCATTGTCAACTTGGGCCAGTCGTAATGTGTAAAAAAGCAGCCAA
GGCAGGACTCTCTCAATCACTTTTTGAACGTTTAGTTGTTTTGGGCATTCGTCCTTTCCG
CTTGGAAGTTCAATATCGTATGCATCCCGAATTGTCACAATTTCCTTCAAATTTCTTCTA
TGAAGGTTCATTACAAAATGGTGTTTGTGCTGAAGAAAGAAAATTACGTATTGATTTTCC
ATGGCCATCTCCTGAATGTCCGATGTTCTTTCTAGTAACACAAGGTGCTGAAGAAATTGC
TGGAAGTGGTACTTCATATTTGAATCGAACTGAAGCTGCAAATGTCGAAAAAATTACAAC
TAGATTTTTGAAATCGGGTTTGAAGCCAGAACAGATTGGAATCATAACTCCTTATGAAGG
TCAACGAGCATATTTGGTTCAGTACATGCAGTATCAAGGAAGTTTACATAGCAAATTGTA
TCAAGAAATTGAAATTGCATCTGTTGATG
>g3586.t12 Gene=g3586 Length=188
MQSTEPEAMVPVVLGARQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPFRL
EVQYRMHPELSQFPSNFFYEGSLQNGVCAEERKLRIDFPWPSPECPMFFLVTQGAEEIAG
SGTSYLNRTEAANVEKITTRFLKSGLKPEQIGIITPYEGQRAYLVQYMQYQGSLHSKLYQ
EIEIASVD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3586.t12 | CDD | cd18808 | SF1_C_Upf1 | 66 | 188 | 0 |
| 7 | g3586.t12 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 63 | 0 |
| 6 | g3586.t12 | Gene3D | G3DSA:3.40.50.300 | - | 64 | 188 | 0 |
| 3 | g3586.t12 | PANTHER | PTHR10887 | DNA2/NAM7 HELICASE FAMILY | 2 | 188 | 0 |
| 4 | g3586.t12 | PANTHER | PTHR10887:SF486 | REGULATOR OF NONSENSE TRANSCRIPTS 1-LIKE PROTEIN | 2 | 188 | 0 |
| 1 | g3586.t12 | Pfam | PF13086 | AAA domain | 2 | 33 | 0 |
| 2 | g3586.t12 | Pfam | PF13087 | AAA domain | 42 | 188 | 0 |
| 5 | g3586.t12 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 172 | 0 |
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:0004386 | helicase activity | 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.
