General information for g11784.t32
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t32 | TSS | g11784.t32 | 18397454 | 18397454 |
| chr_1 | g11784 | g11784.t32 | isoform | g11784.t32 | 18397547 | 18398945 |
| chr_1 | g11784 | g11784.t32 | exon | g11784.t32.exon1 | 18397547 | 18398098 |
| chr_1 | g11784 | g11784.t32 | cds | g11784.t32.CDS1 | 18397983 | 18398098 |
| chr_1 | g11784 | g11784.t32 | exon | g11784.t32.exon2 | 18398155 | 18398363 |
| chr_1 | g11784 | g11784.t32 | cds | g11784.t32.CDS2 | 18398155 | 18398363 |
| chr_1 | g11784 | g11784.t32 | exon | g11784.t32.exon3 | 18398430 | 18398640 |
| chr_1 | g11784 | g11784.t32 | cds | g11784.t32.CDS3 | 18398430 | 18398640 |
| chr_1 | g11784 | g11784.t32 | exon | g11784.t32.exon4 | 18398704 | 18398945 |
| chr_1 | g11784 | g11784.t32 | cds | g11784.t32.CDS4 | 18398704 | 18398944 |
| chr_1 | g11784 | g11784.t32 | TTS | g11784.t32 | 18398940 | 18398940 |
Sequences
>g11784.t32 Gene=g11784 Length=1214
ATGAAACCAATAGCAGCAGATGAAATGTTTCCAGAAGGAATTGATGTAGACGATGTAAGT
TTAAATTATTAAAAAAAATGATTGAAATATTTTTATTTTTTTTTAAAATTTATGATATTT
CATATAAAAGCAGAGTGCAGTAGTTCTTGATAGTCTTCATGATGGTCAGAAAGATATACA
TTCAGATTTCTTTAATGGTAATTTCTTATTTTCTAAGAAATATTTTAAAAAGTTACTAAA
CAAAAATATATTGTACATTATTTTTTAGATTTCGATGATTTATTTGATGAAGAGGAGTGA
GATAGCAACGCATTATTTCTTATTTTTGTGATTTTCTCATATATTATTATGCATTAAAAA
AATAAAAATTATTTGAATTACTTCTACATGTAGAACTGTGTATTTTTGTTTTGTTTACAA
ATTTCATCTATCGGCAATGTTGAGATTTTCAAAATTAATTGATATATCAAGATATAAACA
TATATTTCACAAATGTAAATTACATAGCAGTTCCACATCAAAATATGAAGCAAACGTTGA
GTTTAGCAATGGGCGAAAGATGACATTTAATACGGGAAATTTAGCTAAATTTACTGATGG
ATGCGTGGTTGTGAAAACAGGCGATACAGCAGTAATGTGCACAGCAATAAGTAGCAAAAA
GGCATCTAGTTCTGCTTCATTTCTTCCATTATCTGTCGATTATAGGTTAAAAAGTAGCGC
TGCCGGTCGAATACCAACAAATTACATGCGAAGAGAATTTGGGTCAACTGAAAAAGAAAT
TTTAGCATCACGTTTAGTTGATCGATCTATTAGGCCACTATTTTCAAAAGATTATCGTTT
TGAAACTCAAATAGTATGCAATGTTCTCTCTGTCGATTCTTTAAATAAACCTGATGTTAA
TGCAATTAATGCTGCTTCAGCAGCCCTTCATTTAAGCGACATTCCATGGAATGGTCCTAT
AGGCGCAGTGAGAGTTGGATTATTCAAAAATGATCTGATAATAAATCCAACAAGACGAGA
ACTTCAGGTATCAGACTTGGATTTGATAGTTGTTGCAACAAAACAAAATTTAGTTGTAAT
GCTTGAAGGACGAGGAAACATTGTTTTGTTACCAAACATATTGAAAGCAATTAAGCAAGG
AACTCGTGAAGCTCAATTTATAATAGATAAAATTGAAAAAATGCGAAAAGAATTGCCAAA
TGTAAAACCAAAAA
>g11784.t32 Gene=g11784 Length=259
MLRFSKLIDISRYKHIFHKCKLHSSSTSKYEANVEFSNGRKMTFNTGNLAKFTDGCVVVK
TGDTAVMCTAISSKKASSSASFLPLSVDYRLKSSAAGRIPTNYMRREFGSTEKEILASRL
VDRSIRPLFSKDYRFETQIVCNVLSVDSLNKPDVNAINAASAALHLSDIPWNGPIGAVRV
GLFKNDLIINPTRRELQVSDLDLIVVATKQNLVVMLEGRGNIVLLPNILKAIKQGTREAQ
FIIDKIEKMRKELPNVKPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11784.t32 | Coils | Coil | Coil | 232 | 252 | - |
| 7 | g11784.t32 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 12 | 254 | 2.9E-71 |
| 3 | g11784.t32 | PANTHER | PTHR11252 | POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE | 30 | 255 | 1.0E-80 |
| 4 | g11784.t32 | PANTHER | PTHR11252:SF0 | POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL | 30 | 255 | 1.0E-80 |
| 2 | g11784.t32 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 40 | 170 | 2.9E-18 |
| 1 | g11784.t32 | Pfam | PF03725 | 3’ exoribonuclease family, domain 2 | 173 | 236 | 1.8E-13 |
| 5 | g11784.t32 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 38 | 170 | 3.19E-40 |
| 6 | g11784.t32 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 164 | 253 | 9.29E-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.
