General information for g1703.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Exosome complex component RRP43.
Parent gene
- The parent gene g1703 is located on chr_3: 12608183..12609050 (+ 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 | g1703 | g1703.t2 | TSS | g1703.t2 | 12608132 | 12608132 |
| chr_3 | g1703 | g1703.t2 | isoform | g1703.t2 | 12608183 | 12609050 |
| chr_3 | g1703 | g1703.t2 | exon | g1703.t2.exon1 | 12608183 | 12608209 |
| chr_3 | g1703 | g1703.t2 | exon | g1703.t2.exon2 | 12608261 | 12609050 |
| chr_3 | g1703 | g1703.t2 | cds | g1703.t2.CDS1 | 12608556 | 12609050 |
| chr_3 | g1703 | g1703.t2 | TTS | g1703.t2 | 12609102 | 12609102 |
Sequences
>g1703.t2 Gene=g1703 Length=817
ATGTCACAAGAAAATCTATTCAAGTAAAGCAATAAATCCAGTTAAATTTGTTCTTGATCA
TCTTGAAAAGAATGTGAGACCGGATGGAAGAGAATTTAATGAATTCCGAGCGACAATCAT
AAACAAAGATTCCATATCGCGTGCAGAAGGGTCAGCTTTAGTTAAAATAGGAAATACTAC
TGTTTTATGTGGAATTAAAGCAGAATTAGCAGAACCAGACAATATAGATCAAAATATTGG
CTTTATTGTCCCAAATATTGAACTTTCAAAGCTTTGTTCACCAAAATATCGAGCGATTGG
TGTTTCAGTTGATTCGCAAGTCATGAGTCAAACTATTTTCAATATAATTGTGAATTCAGA
ATGCATCGATCCAGCTGATTTATGTATAGCAAAAGGAAAACTCGTATGGGTGTTATATTG
TGATTTGGTGTGTTTAGATGATGATGGTTCAGTTTTGGATGTTGCTATTCTTGCTCTGTC
AACTGCTCTCAAGTCATTAAAATTACCAAAAGTTGATTTTGACATTGACACTAAAGTAAT
TAAAGTAAACGATAAGATCAGAAGTCCATTAAAACTCAAATGTTTGCCGGTGGCAAGTTC
ATTCATTATTTTCGAAAATGATTATCTACTTGTTGATCCGAGTTCTGATGAAGAAAATAT
TGCAGATACCACTGTGACAGTGTCTACAAGCGATGGAAAAATAAATTACATTCATCAGCC
TGGAGGAAATTCGATTGAACCTGCTAAATTTGATAATATTGTTAGGCAAGCAATTAATCG
TGAAAAATATATAAAATCTTTGCTTGATTCAATATAA
>g1703.t2 Gene=g1703 Length=164
MSQTIFNIIVNSECIDPADLCIAKGKLVWVLYCDLVCLDDDGSVLDVAILALSTALKSLK
LPKVDFDIDTKVIKVNDKIRSPLKLKCLPVASSFIIFENDYLLVDPSSDEENIADTTVTV
STSDGKINYIHQPGGNSIEPAKFDNIVRQAINREKYIKSLLDSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1703.t2 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 1 | 164 | 0.0e+00 |
| 3 | g1703.t2 | PANTHER | PTHR11097 | EXOSOME COMPLEX EXONUCLEASE RIBOSOMAL RNA PROCESSING PROTEIN | 2 | 163 | 0.0e+00 |
| 4 | g1703.t2 | PANTHER | PTHR11097:SF9 | EXOSOME COMPLEX COMPONENT RRP43 | 2 | 163 | 0.0e+00 |
| 2 | g1703.t2 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 11 | 62 | 6.0e-07 |
| 1 | g1703.t2 | Pfam | PF03725 | 3’ exoribonuclease family, domain 2 | 88 | 150 | 2.4e-06 |
| 5 | g1703.t2 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 2 | 112 | 0.0e+00 |
| 6 | g1703.t2 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 83 | 163 | 0.0e+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:0006401 | RNA catabolic process | BP |
| GO:0006396 | RNA processing | BP |
| GO:0000178 | exosome (RNase complex) | CC |
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. There were no conditions that were differentially expressed