General information for g4669.t1
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.t1 | TTS | g4669.t1 | 4039111 | 4039111 |
| chr_2 | g4669 | g4669.t1 | isoform | g4669.t1 | 4039190 | 4039879 |
| chr_2 | g4669 | g4669.t1 | exon | g4669.t1.exon1 | 4039190 | 4039674 |
| chr_2 | g4669 | g4669.t1 | cds | g4669.t1.CDS1 | 4039190 | 4039674 |
| chr_2 | g4669 | g4669.t1 | exon | g4669.t1.exon2 | 4039728 | 4039763 |
| chr_2 | g4669 | g4669.t1 | cds | g4669.t1.CDS2 | 4039728 | 4039763 |
| chr_2 | g4669 | g4669.t1 | exon | g4669.t1.exon3 | 4039825 | 4039879 |
| chr_2 | g4669 | g4669.t1 | cds | g4669.t1.CDS3 | 4039825 | 4039879 |
| chr_2 | g4669 | g4669.t1 | TSS | g4669.t1 | 4040003 | 4040003 |
Sequences
>g4669.t1 Gene=g4669 Length=576
ATGGCAGCAGCTACTAAAGGACGTCAAATTGTTTGGATGGATATGGAAATGACTGGATTA
GAATACAAAAGAGATCGAGTTTTGCAAATAGCAATGCTAATCACCGATCTAAATTTGAAT
ATAATATCAAGAGAATTTCTTGTTACCATTCATCAAGATAAGGAAGTACTTGATAAAATG
AATGATTGGTGCAAAGAGAATCTTAAAGAAATTGCTGAAGAAAGCTTAAAATCTAAAATC
ACTGAAGCTGATGCTGAAAAAATGATGATAGATTTTTTCAATGACAACAAAATTTTACCT
AAAAATAATCCTTTGGCAGGAAATACAATTTATATGGACAGACTTTTTCTTAGAGAATAT
TTTCCTAAAGTCAATGATCATCTGCATTATAGATTAATTGATGTTAGTACAATTAAAGAA
CTTTGTTCTAGATGGAATAAACCGGTTTATCAAAGAGCACCGGAAAAGAAGAATGCACAT
CATGCATTGAGTGATATTAAGAATAGTATAGAAGAATTAAAGTACTATAAAGAAGGATTT
TTAAAAATAGCAACTGATGAAGAGAACAAAGAATAA
>g4669.t1 Gene=g4669 Length=191
MAAATKGRQIVWMDMEMTGLEYKRDRVLQIAMLITDLNLNIISREFLVTIHQDKEVLDKM
NDWCKENLKEIAEESLKSKITEADAEKMMIDFFNDNKILPKNNPLAGNTIYMDRLFLREY
FPKVNDHLHYRLIDVSTIKELCSRWNKPVYQRAPEKKNAHHALSDIKNSIEELKYYKEGF
LKIATDEENKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4669.t1 | CDD | cd06135 | Orn | 10 | 181 | 0 |
| 6 | g4669.t1 | Gene3D | G3DSA:3.30.420.10 | - | 2 | 189 | 0 |
| 2 | g4669.t1 | PANTHER | PTHR11046 | OLIGORIBONUCLEASE, MITOCHONDRIAL | 6 | 190 | 0 |
| 3 | g4669.t1 | PANTHER | PTHR11046:SF19 | - | 6 | 190 | 0 |
| 1 | g4669.t1 | Pfam | PF00929 | Exonuclease | 11 | 172 | 0 |
| 5 | g4669.t1 | SMART | SM00479 | exoiiiendus | 9 | 182 | 0 |
| 4 | g4669.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 7 | 182 | 0 |
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 transcript has been annotated with K13288 (oligoribonuclease [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.
