General information for g3586.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t13 | isoform | g3586.t13 | 26561243 | 26562755 |
| chr_3 | g3586 | g3586.t13 | exon | g3586.t13.exon1 | 26561243 | 26561252 |
| chr_3 | g3586 | g3586.t13 | exon | g3586.t13.exon2 | 26561364 | 26562755 |
| chr_3 | g3586 | g3586.t13 | cds | g3586.t13.CDS1 | 26561387 | 26562256 |
| chr_3 | g3586 | g3586.t13 | TTS | g3586.t13 | 26562742 | 26562742 |
| chr_3 | g3586 | g3586.t13 | TSS | g3586.t13 | NA | NA |
Sequences
>g3586.t13 Gene=g3586 Length=1402
GCTTTTCAAGGTCGGGAGAAAGACATAATAATTATGTCTTGTGTTCGATCAAATGAACAT
CAAGGAATTGGTTTTCTTAATGATCCAAGACGTTTAAATGTGGCTTTGACTCGTGCGAAA
TACGGAATTATTATTGTTGGAAATCCTAAAGTACTTTCGAAGCAACAATTATGGAATAAT
TTGTTGAATTTCTATAAAGAAAAGAAAGTTTTGGTTGAGGGATCGTTGAATAATCTAAAA
GAGTCGATGATTCAATTCGCAAAGCCTAAGAAAATTGTTAATACTTTCAATCCCGGTCAA
CATTTCATGTCATCTACAACATTTGATGCAAAAGAAGCAATGCAACGTCCTCCTTTTTAT
GGAGTAGGTGGTAGTAACAACAATAATAATGATCGCATGATGCATAATAATATGGGAATT
GGTAATCAATGGAATAATAATCATACAATGGATGGAATGTTCAGAGCTCATGATTCAATT
TCGTACATCTCACCAGAACGTGCGCAAGCTGCAATGAATGGTCTTTCTGTTCCAGTAGGC
ATGTTCATGAATATGTCATCAAATAATATGCCTCCTCGATATTTCCAACAGCAACAAGCT
GCTATTCAACAAGCAGCTAAGCAAAGTCGTATGAAGAAAAATATGAGTTCTGGAGGATCT
AGCAGTAGCAACAATAATATGAATGCTGGAAATTCTCAAAGTAAATTGCGTGGTAGAAAC
AGTCAAGCTGGACCATTAACTCAAGGAATGAGTCAAATGATGAGTCAACCTGGATTCAAT
GTTGATTTTTCACAAGGCGACTACACTGGCGAATCTCAAATTGATGGATTATTATCACAA
GATTTCGCTAACAGTCAAGGTCCAGACAAATTTTATAGTAATTTCCAATCGCAAAATTTT
TGATGAACGATTCACATTAATTGTTATTTGAAAACAATAATGTAAAATCTAAATGACATG
GAGTCAGAAATCACTAAAGTAATTTTGAGTGAAGGCATTGATTTGGAAGAACCGTTCATA
AGACTCATAATATAAATGACTTCAATACTATAATATACGAATATGGCAAGGCTCTCTCAT
CTGGAGCGGAAGTATTGAGTAGCCGGGTTGGTTTAGATTAAATACACACATACGACAATT
ATGATGCAAAAGTCATGCAACAAAATGTGCTTTGTGGAAAAAACAATAAAGAGCAAAATT
GTCATCATCGCTCATCATTCATACCCAACAAAATGTGCTTTTCAACTGAGAGACTCGAGT
TAAAATTTTAAAAGAAAGCAAAAAATATAATTTCTAAATAATCCTTTTCACTTTTATTTT
ATTATTTTACAAAATTGTTGCAAATATTATTCCAAAATTTTCAAAACCTTAATAAATTCG
ACAATTTGAAATCAAAGATTTG
>g3586.t13 Gene=g3586 Length=289
MSCVRSNEHQGIGFLNDPRRLNVALTRAKYGIIIVGNPKVLSKQQLWNNLLNFYKEKKVL
VEGSLNNLKESMIQFAKPKKIVNTFNPGQHFMSSTTFDAKEAMQRPPFYGVGGSNNNNND
RMMHNNMGIGNQWNNNHTMDGMFRAHDSISYISPERAQAAMNGLSVPVGMFMNMSSNNMP
PRYFQQQQAAIQQAAKQSRMKKNMSSGGSSSSNNNMNAGNSQSKLRGRNSQAGPLTQGMS
QMMSQPGFNVDFSQGDYTGESQIDGLLSQDFANSQGPDKFYSNFQSQNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3586.t13 | CDD | cd18808 | SF1_C_Upf1 | 1 | 55 | 1.10762E-24 |
| 5 | g3586.t13 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 76 | 7.3E-25 |
| 4 | g3586.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 185 | 231 | - |
| 2 | g3586.t13 | PANTHER | PTHR10887 | DNA2/NAM7 HELICASE FAMILY | 1 | 84 | 8.0E-39 |
| 3 | g3586.t13 | PANTHER | PTHR10887:SF486 | REGULATOR OF NONSENSE TRANSCRIPTS 1-LIKE PROTEIN | 1 | 84 | 8.0E-39 |
| 1 | g3586.t13 | Pfam | PF13087 | AAA domain | 1 | 38 | 1.3E-14 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
