General information for g10109.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Exosome complex component MTR3.
Parent gene
- The parent gene g10109 is located on chr_1: 7476671..7477597 (- 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 | g10109 | g10109.t1 | TTS | g10109.t1 | 7476646 | 7476646 |
| chr_1 | g10109 | g10109.t1 | isoform | g10109.t1 | 7476671 | 7477597 |
| chr_1 | g10109 | g10109.t1 | exon | g10109.t1.exon1 | 7476671 | 7477220 |
| chr_1 | g10109 | g10109.t1 | cds | g10109.t1.CDS1 | 7476671 | 7477220 |
| chr_1 | g10109 | g10109.t1 | exon | g10109.t1.exon2 | 7477277 | 7477394 |
| chr_1 | g10109 | g10109.t1 | cds | g10109.t1.CDS2 | 7477277 | 7477394 |
| chr_1 | g10109 | g10109.t1 | exon | g10109.t1.exon3 | 7477450 | 7477597 |
| chr_1 | g10109 | g10109.t1 | cds | g10109.t1.CDS3 | 7477450 | 7477597 |
| chr_1 | g10109 | g10109.t1 | TSS | g10109.t1 | 7477658 | 7477658 |
Sequences
>g10109.t1 Gene=g10109 Length=816
ATGCCATTTGATCAAAAGAAAATCAATGGTCCAGATAATTCTTTTTCATATAAACAATAC
ATAGAATCGAATAAGGAAGAAAATCAAGATTTTGAGCTTAAGAAAGGACGAAAAGATGGT
CGAGAACCTAATGAAAGCCGTAAAATTGCTGTTCAAATGAATGCTATATCAAAAGCAAAA
GGATCTTGTTATATTGAAAATGGTAATACAAAGCTAATTTGTGGAGTTTTTGAATTGCGT
GAAATTTCAAGATCAACACGATATAATGATAAAGGACAACTCTATTGCGATTTTAAATAT
GCTCCATTTTCGAGAGATAATCGGAAATCACTTAATGAAAATGATGAAAAATTAATCTCA
AACAGCATAAAAACAGCTCTAGAATCTGTAGTTTGTCTTCATGAGTTTCCGAATTATCAA
ATTGATATTTTTATAATGGTATTGGAAGATGATGGTTCTATTTTATCGACTGCAATTATG
GCTGCTGGAGTTGCATTTATTGATGCTTGTATTCCTTGCTTTGATATACCTGCTTCATCA
ACGATTGCATTTTACGATGGAAAAGCACTTGTTGATCCAACAGCAGAAGAAGAAGAAATT
GTAAATACATCAAATCCACAAAATAATCATGGAACAATCACATTAACTTCACTTAATTCG
ATTGATCAAGTTGCACAAATTCTCTTTACTGGTTACATTGAGCCTTCAATATTGAAAGAA
GCAAAGAGGCAGTTACTTGAAAATAACAAAATTCATGAAAAATATCTCAAAAAAGTAATC
AGTATGAAAATTGTGAAAGAGAATCGTGAGAGTTAA
>g10109.t1 Gene=g10109 Length=271
MPFDQKKINGPDNSFSYKQYIESNKEENQDFELKKGRKDGREPNESRKIAVQMNAISKAK
GSCYIENGNTKLICGVFELREISRSTRYNDKGQLYCDFKYAPFSRDNRKSLNENDEKLIS
NSIKTALESVVCLHEFPNYQIDIFIMVLEDDGSILSTAIMAAGVAFIDACIPCFDIPASS
TIAFYDGKALVDPTAEEEEIVNTSNPQNNHGTITLTSLNSIDQVAQILFTGYIEPSILKE
AKRQLLENNKIHEKYLKKVISMKIVKENRES
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10109.t1 | CDD | cd11371 | RNase_PH_MTR3 | 46 | 252 | 0 |
| 6 | g10109.t1 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 2 | 268 | 0 |
| 2 | g10109.t1 | PANTHER | PTHR11953 | EXOSOME COMPLEX COMPONENT | 20 | 258 | 0 |
| 3 | g10109.t1 | PANTHER | PTHR11953:SF2 | EXOSOME COMPLEX COMPONENT MTR3 | 20 | 258 | 0 |
| 1 | g10109.t1 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 45 | 172 | 0 |
| 4 | g10109.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 34 | 199 | 0 |
| 5 | g10109.t1 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 174 | 260 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K12587 (exosome complex component MTR3)
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.
