General information for g1703.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g1703.t1 | 12608132 | 12608132 |
| chr_3 | g1703 | g1703.t1 | isoform | g1703.t1 | 12608183 | 12609050 |
| chr_3 | g1703 | g1703.t1 | exon | g1703.t1.exon1 | 12608183 | 12608205 |
| chr_3 | g1703 | g1703.t1 | cds | g1703.t1.CDS1 | 12608183 | 12608205 |
| chr_3 | g1703 | g1703.t1 | exon | g1703.t1.exon2 | 12608261 | 12609050 |
| chr_3 | g1703 | g1703.t1 | cds | g1703.t1.CDS2 | 12608261 | 12609050 |
| chr_3 | g1703 | g1703.t1 | TTS | g1703.t1 | 12609102 | 12609102 |
Sequences
>g1703.t1 Gene=g1703 Length=813
ATGTCACAAGAAAATCTATTCAAAGCAATAAATCCAGTTAAATTTGTTCTTGATCATCTT
GAAAAGAATGTGAGACCGGATGGAAGAGAATTTAATGAATTCCGAGCGACAATCATAAAC
AAAGATTCCATATCGCGTGCAGAAGGGTCAGCTTTAGTTAAAATAGGAAATACTACTGTT
TTATGTGGAATTAAAGCAGAATTAGCAGAACCAGACAATATAGATCAAAATATTGGCTTT
ATTGTCCCAAATATTGAACTTTCAAAGCTTTGTTCACCAAAATATCGAGCGATTGGTGTT
TCAGTTGATTCGCAAGTCATGAGTCAAACTATTTTCAATATAATTGTGAATTCAGAATGC
ATCGATCCAGCTGATTTATGTATAGCAAAAGGAAAACTCGTATGGGTGTTATATTGTGAT
TTGGTGTGTTTAGATGATGATGGTTCAGTTTTGGATGTTGCTATTCTTGCTCTGTCAACT
GCTCTCAAGTCATTAAAATTACCAAAAGTTGATTTTGACATTGACACTAAAGTAATTAAA
GTAAACGATAAGATCAGAAGTCCATTAAAACTCAAATGTTTGCCGGTGGCAAGTTCATTC
ATTATTTTCGAAAATGATTATCTACTTGTTGATCCGAGTTCTGATGAAGAAAATATTGCA
GATACCACTGTGACAGTGTCTACAAGCGATGGAAAAATAAATTACATTCATCAGCCTGGA
GGAAATTCGATTGAACCTGCTAAATTTGATAATATTGTTAGGCAAGCAATTAATCGTGAA
AAATATATAAAATCTTTGCTTGATTCAATATAA
>g1703.t1 Gene=g1703 Length=270
MSQENLFKAINPVKFVLDHLEKNVRPDGREFNEFRATIINKDSISRAEGSALVKIGNTTV
LCGIKAELAEPDNIDQNIGFIVPNIELSKLCSPKYRAIGVSVDSQVMSQTIFNIIVNSEC
IDPADLCIAKGKLVWVLYCDLVCLDDDGSVLDVAILALSTALKSLKLPKVDFDIDTKVIK
VNDKIRSPLKLKCLPVASSFIIFENDYLLVDPSSDEENIADTTVTVSTSDGKINYIHQPG
GNSIEPAKFDNIVRQAINREKYIKSLLDSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1703.t1 | CDD | cd11369 | RNase_PH_RRP43 | 8 | 267 | 0.0e+00 |
| 7 | g1703.t1 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 3 | 270 | 0.0e+00 |
| 3 | g1703.t1 | PANTHER | PTHR11097 | EXOSOME COMPLEX EXONUCLEASE RIBOSOMAL RNA PROCESSING PROTEIN | 9 | 269 | 0.0e+00 |
| 4 | g1703.t1 | PANTHER | PTHR11097:SF9 | EXOSOME COMPLEX COMPONENT RRP43 | 9 | 269 | 0.0e+00 |
| 2 | g1703.t1 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 33 | 168 | 0.0e+00 |
| 1 | g1703.t1 | Pfam | PF03725 | 3’ exoribonuclease family, domain 2 | 194 | 256 | 6.3e-06 |
| 5 | g1703.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 5 | 218 | 0.0e+00 |
| 6 | g1703.t1 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 189 | 269 | 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 transcript has been annotated with K12586 (exosome complex component RRP43)
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.
