General information for g1758.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative exonuclease GOR.
Parent gene
- The parent gene g1758 is located on chr_3: 12875380..12876418 (+ 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 | g1758 | g1758.t4 | isoform | g1758.t4 | 12875380 | 12876109 |
| chr_3 | g1758 | g1758.t4 | exon | g1758.t4.exon1 | 12875380 | 12875910 |
| chr_3 | g1758 | g1758.t4 | cds | g1758.t4.CDS1 | 12875469 | 12875910 |
| chr_3 | g1758 | g1758.t4 | exon | g1758.t4.exon2 | 12876027 | 12876109 |
| chr_3 | g1758 | g1758.t4 | cds | g1758.t4.CDS2 | 12876027 | 12876109 |
| chr_3 | g1758 | g1758.t4 | TTS | g1758.t4 | 12876257 | 12876257 |
| chr_3 | g1758 | g1758.t4 | TSS | g1758.t4 | NA | NA |
Sequences
>g1758.t4 Gene=g1758 Length=614
CAATAGCCGGAAGTACAGGATGTTGTTACGCTGACTATCACGTATTTGATTATATCGATT
ATAATAATCTCGTTGGATATGTCAAAACAATGGATAAAGATGAAAATTATGTGTGCACAA
AAAAAGATATTTTTGCATTAGATTGTGAAATGTGCTATACAGTATGTGGTTTTGAATTGA
CACGTTTGACAATTGTCGATTATGATGAGAAAGTTGTTTATGATAAATTCGTCCGACCAC
AAAATCGTGTAATTGACTATAATACAAGATACTCTGGAATAACGGAAGCAACTTTATCTT
CAAAAGATGCGTTAACACTTCCTGAAATTCAAGCAGTATTATTATCATTATTTCACTCGA
GGACTATATTAATTGGACATTCACTTGAAAGTGATTTCAAGAGTCTAAAATTAATACACT
CTACTGTTGTTGATACATCTGTTTTGTATCCACATAAAATGGGATTTCCTAAAAAGAGAG
CTTTAAAAACATTATGCATTGAATATTTGAAAAAGATCATACAAGAAGATGACGCCGGTC
ACGATTCTGCTGAAGATTCAACAGTGTGCATTCAATTGGTAAAAAATTATTTGAGGAATC
GTATTGTCAATTGA
>g1758.t4 Gene=g1758 Length=174
MDKDENYVCTKKDIFALDCEMCYTVCGFELTRLTIVDYDEKVVYDKFVRPQNRVIDYNTR
YSGITEATLSSKDALTLPEIQAVLLSLFHSRTILIGHSLESDFKSLKLIHSTVVDTSVLY
PHKMGFPKKRALKTLCIEYLKKIIQEDDAGHDSAEDSTVCIQLVKNYLRNRIVN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1758.t4 | CDD | cd06145 | REX1_like | 15 | 165 | 0e+00 |
| 6 | g1758.t4 | Gene3D | G3DSA:3.30.420.10 | - | 8 | 173 | 0e+00 |
| 2 | g1758.t4 | PANTHER | PTHR12801:SF138 | FI18136P1-RELATED | 5 | 169 | 0e+00 |
| 3 | g1758.t4 | PANTHER | PTHR12801 | RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATED | 5 | 169 | 0e+00 |
| 1 | g1758.t4 | Pfam | PF00929 | Exonuclease | 28 | 163 | 9e-07 |
| 5 | g1758.t4 | SMART | SM00479 | exoiiiendus | 13 | 173 | 0e+00 |
| 4 | g1758.t4 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 14 | 170 | 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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14570 (RNA exonuclease [EC:3.1.-.-])
Pathway
- This transcript belongs to the following pathways
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.
