General information for g3586.t4
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.t4 | TSS | g3586.t4 | 26557947 | 26557947 |
| chr_3 | g3586 | g3586.t4 | isoform | g3586.t4 | 26558107 | 26559573 |
| chr_3 | g3586 | g3586.t4 | exon | g3586.t4.exon1 | 26558107 | 26558250 |
| chr_3 | g3586 | g3586.t4 | cds | g3586.t4.CDS1 | 26558107 | 26558250 |
| chr_3 | g3586 | g3586.t4 | exon | g3586.t4.exon2 | 26558597 | 26559003 |
| chr_3 | g3586 | g3586.t4 | cds | g3586.t4.CDS2 | 26558597 | 26559003 |
| chr_3 | g3586 | g3586.t4 | exon | g3586.t4.exon3 | 26559071 | 26559573 |
| chr_3 | g3586 | g3586.t4 | cds | g3586.t4.CDS3 | 26559071 | 26559572 |
| chr_3 | g3586 | g3586.t4 | TTS | g3586.t4 | NA | NA |
Sequences
>g3586.t4 Gene=g3586 Length=1054
ATGTCATTCAGCCAAAGTCTATCTTTTCAAGATGATGATGATTTTATTTCGCAACCTTTC
TCGCAATTTAACTTTCAAGACTTTACACTTCCAAGTCAGACACAACAGTCTCAATTATCT
CAATTAGATCACATTGGAAACCAGCTGAATGGATTCGATGCTAAAGTAGATTCATCGCCA
GTTGCTTCTAGCAGCAAAATTAATGCAATCACCTCTGGTCTCAATGACCTGCAATTTGAA
GAAGAAGATGATGAACAGATAACATCAAAAGAGTTGGCTGCACATAGCTGTCGCTATTGT
GGTATTAGTGAACCATCGACAGTTGTCATGTGCAATATATGTAAAAAATGGTTTTGTAAT
GCCCGTGGTAATACATCTGGTTCTCATATATTGCATCATCTCGTTCGTGCTAAACATCGT
GAAGTAACTTTGCATGAAGATGGACCACTTGGCAGCACTGTTCTTGAATGCTATTCATGT
GGTATTCGAAATGTTTTCGTTTTAGGATTTATTCCAGCTAAGGCAGATTCTGTCGTTGTT
CTTCTTTGTCGTCAACCATGTGCTTCACAAAATTCATTAAAAGATATGAATTGGGATCAA
GATCAATGGAAACCTTTAATTTCTGATCGCTGTTTCTTGCCATGGCTTGTGAAAATTCCA
ACTGAACAGGAACAACTGCGTGCTCGTCAAATAACAGCTACAACTATCAATAAACTTGAA
GAACTTTGGAAAGAAAATGTAGAGGCATCTATATCTGATTTAGAAAAACCGGGAATTGAT
AAGGAACCCTCACAAGTTCAACTACGTTATGACGATGGTTATCAATATCAAAACATATTT
GGCCCACTTGTAAAGTTAGAGGCCGATTATGATAAACGCTTAAAAGAGTCTCAGACTCAA
GAAAATATAGAAGTTCGTTGGGATACTGGTTTAAATAAGAAAATAATTGCATATTTCACT
TTACCTAAAATTGATTCAGATATGAAGTTAATGGCTGGCGATGAATTGCGGTTACGATAT
GTTGGCGAGCTTCATGATTCATGGTCTGCAATAG
>g3586.t4 Gene=g3586 Length=351
MSFSQSLSFQDDDDFISQPFSQFNFQDFTLPSQTQQSQLSQLDHIGNQLNGFDAKVDSSP
VASSSKINAITSGLNDLQFEEEDDEQITSKELAAHSCRYCGISEPSTVVMCNICKKWFCN
ARGNTSGSHILHHLVRAKHREVTLHEDGPLGSTVLECYSCGIRNVFVLGFIPAKADSVVV
LLCRQPCASQNSLKDMNWDQDQWKPLISDRCFLPWLVKIPTEQEQLRARQITATTINKLE
ELWKENVEASISDLEKPGIDKEPSQVQLRYDDGYQYQNIFGPLVKLEADYDKRLKESQTQ
ENIEVRWDTGLNKKIIAYFTLPKIDSDMKLMAGDELRLRYVGELHDSWSAI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3586.t4 | CDD | cd21400 | ZBD_UPF1-like | 96 | 216 | 0.00e+00 |
| 7 | g3586.t4 | CDD | cd21407 | 1B_UPF1-like | 299 | 351 | 0.00e+00 |
| 6 | g3586.t4 | Gene3D | G3DSA:2.40.30.230 | - | 299 | 351 | 0.00e+00 |
| 3 | g3586.t4 | PANTHER | PTHR10887 | DNA2/NAM7 HELICASE FAMILY | 130 | 349 | 0.00e+00 |
| 4 | g3586.t4 | PANTHER | PTHR10887:SF486 | REGULATOR OF NONSENSE TRANSCRIPTS 1-LIKE PROTEIN | 130 | 349 | 0.00e+00 |
| 1 | g3586.t4 | Pfam | PF09416 | RNA helicase (UPF2 interacting domain) | 95 | 246 | 0.00e+00 |
| 2 | g3586.t4 | Pfam | PF18141 | Domain of unknown function (DUF5599) | 298 | 350 | 0.00e+00 |
| 5 | g3586.t4 | SUPERFAMILY | SSF57850 | RING/U-box | 95 | 162 | 4.94e-05 |
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:0003723 | RNA binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0003724 | RNA helicase activity | MF |
| GO:0008270 | zinc ion binding | MF |
| GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | BP |
| GO:0005737 | cytoplasm | CC |
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.
