General information for g10109.t4
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.t4 | TTS | g10109.t4 | 7476646 | 7476646 |
| chr_1 | g10109 | g10109.t4 | isoform | g10109.t4 | 7476671 | 7477597 |
| chr_1 | g10109 | g10109.t4 | exon | g10109.t4.exon1 | 7476671 | 7477394 |
| chr_1 | g10109 | g10109.t4 | cds | g10109.t4.CDS1 | 7476671 | 7477246 |
| chr_1 | g10109 | g10109.t4 | exon | g10109.t4.exon2 | 7477450 | 7477597 |
| chr_1 | g10109 | g10109.t4 | TSS | g10109.t4 | 7477658 | 7477658 |
Sequences
>g10109.t4 Gene=g10109 Length=872
ATGCCATTTGATCAAAAGAAAATCAATGGTCCAGATAATTCTTTTTCATATAAACAATAC
ATAGAATCGAATAAGGAAGAAAATCAAGATTTTGAGCTTAAGAAAGGACGAAAAGATGGT
CGAGAACCTAATGAAAGCCGTAAAATTGCTGTTCAAATGAATGCTATATCAAAAGCAAAA
GGATCTTGTTATATTGAAAATGGTAATACAAAGCTAATTTGTGGAGTTTTTGAATTGCGT
GAAATTTCAAGATCAACACGATATAAGTAATTTCTCAATCAAGTATAACTCTTAAAATGT
TTAAAAATCATTCTTATTTTAGTGATAAAGGACAACTCTATTGCGATTTTAAATATGCTC
CATTTTCGAGAGATAATCGGAAATCACTTAATGAAAATGATGAAAAATTAATCTCAAACA
GCATAAAAACAGCTCTAGAATCTGTAGTTTGTCTTCATGAGTTTCCGAATTATCAAATTG
ATATTTTTATAATGGTATTGGAAGATGATGGTTCTATTTTATCGACTGCAATTATGGCTG
CTGGAGTTGCATTTATTGATGCTTGTATTCCTTGCTTTGATATACCTGCTTCATCAACGA
TTGCATTTTACGATGGAAAAGCACTTGTTGATCCAACAGCAGAAGAAGAAGAAATTGTAA
ATACATCAAATCCACAAAATAATCATGGAACAATCACATTAACTTCACTTAATTCGATTG
ATCAAGTTGCACAAATTCTCTTTACTGGTTACATTGAGCCTTCAATATTGAAAGAAGCAA
AGAGGCAGTTACTTGAAAATAACAAAATTCATGAAAAATATCTCAAAAAAGTAATCAGTA
TGAAAATTGTGAAAGAGAATCGTGAGAGTTAA
>g10109.t4 Gene=g10109 Length=191
MFKNHSYFSDKGQLYCDFKYAPFSRDNRKSLNENDEKLISNSIKTALESVVCLHEFPNYQ
IDIFIMVLEDDGSILSTAIMAAGVAFIDACIPCFDIPASSTIAFYDGKALVDPTAEEEEI
VNTSNPQNNHGTITLTSLNSIDQVAQILFTGYIEPSILKEAKRQLLENNKIHEKYLKKVI
SMKIVKENRES
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10109.t4 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 3 | 189 | 0.00000 |
| 3 | g10109.t4 | PANTHER | PTHR11953 | EXOSOME COMPLEX COMPONENT | 6 | 179 | 0.00000 |
| 4 | g10109.t4 | PANTHER | PTHR11953:SF2 | EXOSOME COMPLEX COMPONENT MTR3 | 6 | 179 | 0.00000 |
| 2 | g10109.t4 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 10 | 92 | 0.00000 |
| 1 | g10109.t4 | Pfam | PF03725 | 3’ exoribonuclease family, domain 2 | 95 | 143 | 0.00027 |
| 5 | g10109.t4 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 6 | 119 | 0.00000 |
| 6 | g10109.t4 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 94 | 180 | 0.00000 |
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 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.
