General information for g11784.t33
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Polyribonucleotide nucleotidyltransferase 1, mitochondrial.
Parent gene
- The parent gene g11784 is located on chr_1: 18400601..18401710 (+ 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_1 | g11784 | g11784.t33 | TSS | g11784.t33 | 18397454 | 18397454 |
| chr_1 | g11784 | g11784.t33 | isoform | g11784.t33 | 18397547 | 18398945 |
| chr_1 | g11784 | g11784.t33 | exon | g11784.t33.exon1 | 18397547 | 18398098 |
| chr_1 | g11784 | g11784.t33 | exon | g11784.t33.exon2 | 18398155 | 18398252 |
| chr_1 | g11784 | g11784.t33 | cds | g11784.t33.CDS1 | 18398203 | 18398252 |
| chr_1 | g11784 | g11784.t33 | exon | g11784.t33.exon3 | 18398308 | 18398363 |
| chr_1 | g11784 | g11784.t33 | cds | g11784.t33.CDS2 | 18398308 | 18398363 |
| chr_1 | g11784 | g11784.t33 | exon | g11784.t33.exon4 | 18398430 | 18398640 |
| chr_1 | g11784 | g11784.t33 | cds | g11784.t33.CDS3 | 18398430 | 18398640 |
| chr_1 | g11784 | g11784.t33 | exon | g11784.t33.exon5 | 18398704 | 18398945 |
| chr_1 | g11784 | g11784.t33 | cds | g11784.t33.CDS4 | 18398704 | 18398944 |
| chr_1 | g11784 | g11784.t33 | TTS | g11784.t33 | 18398940 | 18398940 |
Sequences
>g11784.t33 Gene=g11784 Length=1159
ATGAAACCAATAGCAGCAGATGAAATGTTTCCAGAAGGAATTGATGTAGACGATGTAAGT
TTAAATTATTAAAAAAAATGATTGAAATATTTTTATTTTTTTTTAAAATTTATGATATTT
CATATAAAAGCAGAGTGCAGTAGTTCTTGATAGTCTTCATGATGGTCAGAAAGATATACA
TTCAGATTTCTTTAATGGTAATTTCTTATTTTCTAAGAAATATTTTAAAAAGTTACTAAA
CAAAAATATATTGTACATTATTTTTTAGATTTCGATGATTTATTTGATGAAGAGGAGTGA
GATAGCAACGCATTATTTCTTATTTTTGTGATTTTCTCATATATTATTATGCATTAAAAA
AATAAAAATTATTTGAATTACTTCTACATGTAGAACTGTGTATTTTTGTTTTGTTTACAA
ATTTCATCTATCGGCAATGTTGAGATTTTCAAAATTAATTGATATATCAAGATATAAACA
TATATTTCACAAATGTAAATTACATAGCAGTTCCACATCAAAATATGAAGCAAACGTTGA
GTTTAGCAATGGGCGAAAGATGACATTTAATACGGGAAATTTAGCTAAATTTACTGATGG
ATGCGTGGTTGTGAAAACAGGCGATACAGCAGTAATGTGCACAGCAATAAGTTAAAAAGT
AGCGCTGCCGGTCGAATACCAACAAATTACATGCGAAGAGAATTTGGGTCAACTGAAAAA
GAAATTTTAGCATCACGTTTAGTTGATCGATCTATTAGGCCACTATTTTCAAAAGATTAT
CGTTTTGAAACTCAAATAGTATGCAATGTTCTCTCTGTCGATTCTTTAAATAAACCTGAT
GTTAATGCAATTAATGCTGCTTCAGCAGCCCTTCATTTAAGCGACATTCCATGGAATGGT
CCTATAGGCGCAGTGAGAGTTGGATTATTCAAAAATGATCTGATAATAAATCCAACAAGA
CGAGAACTTCAGGTATCAGACTTGGATTTGATAGTTGTTGCAACAAAACAAAATTTAGTT
GTAATGCTTGAAGGACGAGGAAACATTGTTTTGTTACCAAACATATTGAAAGCAATTAAG
CAAGGAACTCGTGAAGCTCAATTTATAATAGATAAAATTGAAAAAATGCGAAAAGAATTG
CCAAATGTAAAACCAAAAA
>g11784.t33 Gene=g11784 Length=186
MRGCENRRYSSNVHSNKLKSSAAGRIPTNYMRREFGSTEKEILASRLVDRSIRPLFSKDY
RFETQIVCNVLSVDSLNKPDVNAINAASAALHLSDIPWNGPIGAVRVGLFKNDLIINPTR
RELQVSDLDLIVVATKQNLVVMLEGRGNIVLLPNILKAIKQGTREAQFIIDKIEKMRKEL
PNVKPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11784.t33 | Coils | Coil | Coil | 159 | 179 | - |
| 7 | g11784.t33 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 5 | 181 | 1.9E-51 |
| 3 | g11784.t33 | PANTHER | PTHR11252 | POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE | 19 | 182 | 2.5E-57 |
| 4 | g11784.t33 | PANTHER | PTHR11252:SF0 | POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL | 19 | 182 | 2.5E-57 |
| 2 | g11784.t33 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 24 | 97 | 3.2E-8 |
| 1 | g11784.t33 | Pfam | PF03725 | 3’ exoribonuclease family, domain 2 | 100 | 163 | 9.4E-14 |
| 5 | g11784.t33 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 19 | 97 | 1.27E-24 |
| 6 | g11784.t33 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 91 | 180 | 4.06E-20 |
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:0004654 | polyribonucleotide nucleotidyltransferase activity | MF |
| GO:0006402 | mRNA catabolic process | BP |
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.
