General information for g4669.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Oligoribonuclease.
Parent gene
- The parent gene g4669 is located on chr_2: 4039190..4039879 (- 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_2 | g4669 | g4669.t3 | TTS | g4669.t3 | 4039111 | 4039111 |
| chr_2 | g4669 | g4669.t3 | isoform | g4669.t3 | 4039190 | 4039879 |
| chr_2 | g4669 | g4669.t3 | exon | g4669.t3.exon1 | 4039190 | 4039674 |
| chr_2 | g4669 | g4669.t3 | cds | g4669.t3.CDS1 | 4039190 | 4039672 |
| chr_2 | g4669 | g4669.t3 | exon | g4669.t3.exon2 | 4039797 | 4039879 |
| chr_2 | g4669 | g4669.t3 | TSS | g4669.t3 | 4040003 | 4040003 |
Sequences
>g4669.t3 Gene=g4669 Length=568
ATGGCAGCAGCTACTAAAGGACGTCAAATTGTTTGGATGGATATGGAAATGACTGGTAAA
TTTAAATTTTTCATTTAAAATTGCAATGCTAATCACCGATCTAAATTTGAATATAATATC
AAGAGAATTTCTTGTTACCATTCATCAAGATAAGGAAGTACTTGATAAAATGAATGATTG
GTGCAAAGAGAATCTTAAAGAAATTGCTGAAGAAAGCTTAAAATCTAAAATCACTGAAGC
TGATGCTGAAAAAATGATGATAGATTTTTTCAATGACAACAAAATTTTACCTAAAAATAA
TCCTTTGGCAGGAAATACAATTTATATGGACAGACTTTTTCTTAGAGAATATTTTCCTAA
AGTCAATGATCATCTGCATTATAGATTAATTGATGTTAGTACAATTAAAGAACTTTGTTC
TAGATGGAATAAACCGGTTTATCAAAGAGCACCGGAAAAGAAGAATGCACATCATGCATT
GAGTGATATTAAGAATAGTATAGAAGAATTAAAGTACTATAAAGAAGGATTTTTAAAAAT
AGCAACTGATGAAGAGAACAAAGAATAA
>g4669.t3 Gene=g4669 Length=160
MLITDLNLNIISREFLVTIHQDKEVLDKMNDWCKENLKEIAEESLKSKITEADAEKMMID
FFNDNKILPKNNPLAGNTIYMDRLFLREYFPKVNDHLHYRLIDVSTIKELCSRWNKPVYQ
RAPEKKNAHHALSDIKNSIEELKYYKEGFLKIATDEENKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4669.t3 | CDD | cd06135 | Orn | 1 | 150 | 0.00000 |
| 6 | g4669.t3 | Gene3D | G3DSA:3.30.420.10 | - | 1 | 158 | 0.00000 |
| 2 | g4669.t3 | PANTHER | PTHR11046 | OLIGORIBONUCLEASE, MITOCHONDRIAL | 2 | 159 | 0.00000 |
| 3 | g4669.t3 | PANTHER | PTHR11046:SF19 | - | 2 | 159 | 0.00000 |
| 1 | g4669.t3 | Pfam | PF00929 | Exonuclease | 17 | 141 | 0.00000 |
| 5 | g4669.t3 | SMART | SM00479 | exoiiiendus | 7 | 151 | 0.00094 |
| 4 | g4669.t3 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 2 | 151 | 0.00000 |
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:0000175 | 3’-5’-exoribonuclease activity | MF |
| GO:0003676 | nucleic acid binding | 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.
