General information for g3586.t11
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.t11 | isoform | g3586.t11 | 26560313 | 26562755 |
| chr_3 | g3586 | g3586.t11 | exon | g3586.t11.exon1 | 26560313 | 26560503 |
| chr_3 | g3586 | g3586.t11 | cds | g3586.t11.CDS1 | 26560344 | 26560503 |
| chr_3 | g3586 | g3586.t11 | exon | g3586.t11.exon2 | 26560567 | 26560704 |
| chr_3 | g3586 | g3586.t11 | cds | g3586.t11.CDS2 | 26560567 | 26560704 |
| chr_3 | g3586 | g3586.t11 | exon | g3586.t11.exon3 | 26560764 | 26561252 |
| chr_3 | g3586 | g3586.t11 | cds | g3586.t11.CDS3 | 26560764 | 26561252 |
| chr_3 | g3586 | g3586.t11 | exon | g3586.t11.exon4 | 26561364 | 26562755 |
| chr_3 | g3586 | g3586.t11 | cds | g3586.t11.CDS4 | 26561364 | 26562256 |
| chr_3 | g3586 | g3586.t11 | TTS | g3586.t11 | 26562742 | 26562742 |
| chr_3 | g3586 | g3586.t11 | TSS | g3586.t11 | NA | NA |
Sequences
>g3586.t11 Gene=g3586 Length=2210
CTTTTTGGCATTACATAATCAAATTCGTAACATGGAGACAAATAATGAATATAAAAAGCT
TCAACAATTAAAAGACGAAACTGGTGAATTATCATCGGGTGACGAGAAAAGATATCGTAT
TCTAAAAAAGCAAGCAGAAAAGGAATTATTAGATGCTGCTGATGTCATTTGTTGTACATG
TGTTGGAGCAGGAGATCCACGTCTATCTCGCATAAAGTTCAATTCAATTTTAATTGATGA
GTCAATGCAGAGCACTGAGCCTGAAGCCATGGTTCCAGTCGTTTTGGGCGCACGTCAATT
GATTCTTGTTGGAGATCATTGTCAACTTGGGCCAGTCGTAATGTGTAAAAAAGCAGCCAA
GGCAGGACTCTCTCAATCACTTTTTGAACGTTTAGTTGTTTTGGGCATTCGTCCTTTCCG
CTTGGAAGTTCAATATCGTATGCATCCCGAATTGTCACAATTTCCTTCAAATTTCTTCTA
TGAAGGTTCATTACAAAATGGTGTTTGTGCTGAAGAAAGAAAATTACGTATTGATTTTCC
ATGGCCATCTCCTGAATGTCCGATGTTCTTTCTAGTAACACAAGGTGCTGAAGAAATTGC
TGGAAGTGGTACTTCATATTTGAATCGAACTGAAGCTGCAAATGTCGAAAAAATTACAAC
TAGATTTTTGAAATCGGGTTTGAAGCCAGAACAGATTGGAATCATAACTCCTTATGAAGG
TCAACGAGCATATTTGGTTCAGTACATGCAGTATCAAGGAAGTTTACATAGCAAATTGTA
TCAAGAAATTGAAATTGCATCTGTTGATGCTTTTCAAGGTCGGGAGAAAGACATAATAAT
TATGTCTTGTGTTCGATCAAATGAACATCAAGGAATTGGTTTTCTTAATGATCCAAGACG
TTTAAATGTGGCTTTGACTCGTGCGAAATACGGAATTATTATTGTTGGAAATCCTAAAGT
ACTTTCGAAGCAACAATTATGGAATAATTTGTTGAATTTCTATAAAGAAAAGAAAGTTTT
GGTTGAGGGATCGTTGAATAATCTAAAAGAGTCGATGATTCAATTCGCAAAGCCTAAGAA
AATTGTTAATACTTTCAATCCCGGTCAACATTTCATGTCATCTACAACATTTGATGCAAA
AGAAGCAATGCAACGTCCTCCTTTTTATGGAGTAGGTGGTAGTAACAACAATAATAATGA
TCGCATGATGCATAATAATATGGGAATTGGTAATCAATGGAATAATAATCATACAATGGA
TGGAATGTTCAGAGCTCATGATTCAATTTCGTACATCTCACCAGAACGTGCGCAAGCTGC
AATGAATGGTCTTTCTGTTCCAGTAGGCATGTTCATGAATATGTCATCAAATAATATGCC
TCCTCGATATTTCCAACAGCAACAAGCTGCTATTCAACAAGCAGCTAAGCAAAGTCGTAT
GAAGAAAAATATGAGTTCTGGAGGATCTAGCAGTAGCAACAATAATATGAATGCTGGAAA
TTCTCAAAGTAAATTGCGTGGTAGAAACAGTCAAGCTGGACCATTAACTCAAGGAATGAG
TCAAATGATGAGTCAACCTGGATTCAATGTTGATTTTTCACAAGGCGACTACACTGGCGA
ATCTCAAATTGATGGATTATTATCACAAGATTTCGCTAACAGTCAAGGTCCAGACAAATT
TTATAGTAATTTCCAATCGCAAAATTTTTGATGAACGATTCACATTAATTGTTATTTGAA
AACAATAATGTAAAATCTAAATGACATGGAGTCAGAAATCACTAAAGTAATTTTGAGTGA
AGGCATTGATTTGGAAGAACCGTTCATAAGACTCATAATATAAATGACTTCAATACTATA
ATATACGAATATGGCAAGGCTCTCTCATCTGGAGCGGAAGTATTGAGTAGCCGGGTTGGT
TTAGATTAAATACACACATACGACAATTATGATGCAAAAGTCATGCAACAAAATGTGCTT
TGTGGAAAAAACAATAAAGAGCAAAATTGTCATCATCGCTCATCATTCATACCCAACAAA
ATGTGCTTTTCAACTGAGAGACTCGAGTTAAAATTTTAAAAGAAAGCAAAAAATATAATT
TCTAAATAATCCTTTTCACTTTTATTTTATTATTTTACAAAATTGTTGCAAATATTATTC
CAAAATTTTCAAAACCTTAATAAATTCGACAATTTGAAATCAAAGATTTG
>g3586.t11 Gene=g3586 Length=559
METNNEYKKLQQLKDETGELSSGDEKRYRILKKQAEKELLDAADVICCTCVGAGDPRLSR
IKFNSILIDESMQSTEPEAMVPVVLGARQLILVGDHCQLGPVVMCKKAAKAGLSQSLFER
LVVLGIRPFRLEVQYRMHPELSQFPSNFFYEGSLQNGVCAEERKLRIDFPWPSPECPMFF
LVTQGAEEIAGSGTSYLNRTEAANVEKITTRFLKSGLKPEQIGIITPYEGQRAYLVQYMQ
YQGSLHSKLYQEIEIASVDAFQGREKDIIIMSCVRSNEHQGIGFLNDPRRLNVALTRAKY
GIIIVGNPKVLSKQQLWNNLLNFYKEKKVLVEGSLNNLKESMIQFAKPKKIVNTFNPGQH
FMSSTTFDAKEAMQRPPFYGVGGSNNNNNDRMMHNNMGIGNQWNNNHTMDGMFRAHDSIS
YISPERAQAAMNGLSVPVGMFMNMSSNNMPPRYFQQQQAAIQQAAKQSRMKKNMSSGGSS
SSNNNMNAGNSQSKLRGRNSQAGPLTQGMSQMMSQPGFNVDFSQGDYTGESQIDGLLSQD
FANSQGPDKFYSNFQSQNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3586.t11 | CDD | cd18808 | SF1_C_Upf1 | 137 | 325 | 3.98947E-83 |
| 8 | g3586.t11 | Gene3D | G3DSA:3.40.50.300 | - | 7 | 134 | 1.7E-34 |
| 9 | g3586.t11 | Gene3D | G3DSA:3.40.50.300 | - | 136 | 346 | 4.7E-76 |
| 6 | g3586.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 7 | g3586.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 455 | 501 | - |
| 3 | g3586.t11 | PANTHER | PTHR10887 | DNA2/NAM7 HELICASE FAMILY | 5 | 354 | 9.1E-177 |
| 4 | g3586.t11 | PANTHER | PTHR10887:SF486 | REGULATOR OF NONSENSE TRANSCRIPTS 1-LIKE PROTEIN | 5 | 354 | 9.1E-177 |
| 1 | g3586.t11 | Pfam | PF13086 | AAA domain | 4 | 104 | 1.6E-25 |
| 2 | g3586.t11 | Pfam | PF13087 | AAA domain | 113 | 308 | 3.7E-60 |
| 5 | g3586.t11 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 30 | 329 | 9.3E-51 |
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.
