General information for g3586.t9
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.t9 | isoform | g3586.t9 | 26560067 | 26561743 |
| chr_3 | g3586 | g3586.t9 | exon | g3586.t9.exon1 | 26560067 | 26560249 |
| chr_3 | g3586 | g3586.t9 | exon | g3586.t9.exon2 | 26560310 | 26560503 |
| chr_3 | g3586 | g3586.t9 | exon | g3586.t9.exon3 | 26560578 | 26560704 |
| chr_3 | g3586 | g3586.t9 | cds | g3586.t9.CDS1 | 26560620 | 26560704 |
| chr_3 | g3586 | g3586.t9 | exon | g3586.t9.exon4 | 26560770 | 26561252 |
| chr_3 | g3586 | g3586.t9 | cds | g3586.t9.CDS2 | 26560770 | 26561252 |
| chr_3 | g3586 | g3586.t9 | exon | g3586.t9.exon5 | 26561364 | 26561743 |
| chr_3 | g3586 | g3586.t9 | cds | g3586.t9.CDS3 | 26561364 | 26561743 |
| chr_3 | g3586 | g3586.t9 | TTS | g3586.t9 | 26562742 | 26562742 |
| chr_3 | g3586 | g3586.t9 | TSS | g3586.t9 | NA | NA |
Sequences
>g3586.t9 Gene=g3586 Length=1367
TGGAAAAACTGTTACATCAGCCACAATTGTGTATCAACTTGTAAAAATTAATGGTGGTCC
AGTTTTGGTTTGTGCTCCAAGTAATACAGCAGTTGATCAACTTACTGAAAAAATCCATCG
AACTAATTTAAAAGTAATTCGTGTTTGTGCTAAATCACGTGAAGCAATCGATTCACCTGT
CAGAAGCTTTTTGGCATTACATAATCAAATTCGTAACATGGAGACAAATAATGAATATAA
AAAGCTTCAACAATTAAAAGACGAAACTGGTGAATTATCATCGGGTGACGAGAAAAGATA
TCGTATTCTAAAAAAGCAAGCAGAAAAGGAATTATTAGATGCTGCTGATGTCATTTGTTG
TACATGTGTTGGAGCAGCTATCTCGCATAAAGTTCAATTCAATTTTAATTGATGAGTCAA
TGCAGAGCACTGAGCCTGAAGCCATGGTTCCAGTCGTTTTGGGCGCACGTCAATTGATTC
TTGTTGGAGATCATTGTCAACTTGTCGTAATGTGTAAAAAAGCAGCCAAGGCAGGACTCT
CTCAATCACTTTTTGAACGTTTAGTTGTTTTGGGCATTCGTCCTTTCCGCTTGGAAGTTC
AATATCGTATGCATCCCGAATTGTCACAATTTCCTTCAAATTTCTTCTATGAAGGTTCAT
TACAAAATGGTGTTTGTGCTGAAGAAAGAAAATTACGTATTGATTTTCCATGGCCATCTC
CTGAATGTCCGATGTTCTTTCTAGTAACACAAGGTGCTGAAGAAATTGCTGGAAGTGGTA
CTTCATATTTGAATCGAACTGAAGCTGCAAATGTCGAAAAAATTACAACTAGATTTTTGA
AATCGGGTTTGAAGCCAGAACAGATTGGAATCATAACTCCTTATGAAGGTCAACGAGCAT
ATTTGGTTCAGTACATGCAGTATCAAGGAAGTTTACATAGCAAATTGTATCAAGAAATTG
AAATTGCATCTGTTGATGCTTTTCAAGGTCGGGAGAAAGACATAATAATTATGTCTTGTG
TTCGATCAAATGAACATCAAGGAATTGGTTTTCTTAATGATCCAAGACGTTTAAATGTGG
CTTTGACTCGTGCGAAATACGGAATTATTATTGTTGGAAATCCTAAAGTACTTTCGAAGC
AACAATTATGGAATAATTTGTTGAATTTCTATAAAGAAAAGAAAGTTTTGGTTGAGGGAT
CGTTGAATAATCTAAAAGAGTCGATGATTCAATTCGCAAAGCCTAAGAAAATTGTTAATA
CTTTCAATCCCGGTCAACATTTCATGTCATCTACAACATTTGATGCAAAAGAAGCAATGC
AACGTCCTCCTTTTTATGGAGTAGGTGGTAGTAACAACAATAATAAT
>g3586.t9 Gene=g3586 Length=316
MQSTEPEAMVPVVLGARQLILVGDHCQLVVMCKKAAKAGLSQSLFERLVVLGIRPFRLEV
QYRMHPELSQFPSNFFYEGSLQNGVCAEERKLRIDFPWPSPECPMFFLVTQGAEEIAGSG
TSYLNRTEAANVEKITTRFLKSGLKPEQIGIITPYEGQRAYLVQYMQYQGSLHSKLYQEI
EIASVDAFQGREKDIIIMSCVRSNEHQGIGFLNDPRRLNVALTRAKYGIIIVGNPKVLSK
QQLWNNLLNFYKEKKVLVEGSLNNLKESMIQFAKPKKIVNTFNPGQHFMSSTTFDAKEAM
QRPPFYGVGGSNNNNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3586.t9 | CDD | cd18808 | SF1_C_Upf1 | 64 | 252 | 0.0e+00 |
| 6 | g3586.t9 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 61 | 0.0e+00 |
| 7 | g3586.t9 | Gene3D | G3DSA:3.40.50.300 | - | 63 | 273 | 0.0e+00 |
| 3 | g3586.t9 | PANTHER | PTHR10887 | DNA2/NAM7 HELICASE FAMILY | 2 | 280 | 0.0e+00 |
| 4 | g3586.t9 | PANTHER | PTHR10887:SF486 | REGULATOR OF NONSENSE TRANSCRIPTS 1-LIKE PROTEIN | 2 | 280 | 0.0e+00 |
| 1 | g3586.t9 | Pfam | PF13086 | AAA domain | 2 | 33 | 2.3e-06 |
| 2 | g3586.t9 | Pfam | PF13087 | AAA domain | 40 | 235 | 0.0e+00 |
| 5 | g3586.t9 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 256 | 0.0e+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: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. There were no conditions that were differentially expressed