General information for g6294.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Putative exosome complex component rrp40.
Parent gene
- The parent gene g6294 is located on chr_2: 16017097..16017843 (- 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_2 | g6294 | g6294.t2 | TTS | g6294.t2 | 16016338 | 16016338 |
| chr_2 | g6294 | g6294.t2 | isoform | g6294.t2 | 16016355 | 16017128 |
| chr_2 | g6294 | g6294.t2 | exon | g6294.t2.exon1 | 16016355 | 16016763 |
| chr_2 | g6294 | g6294.t2 | cds | g6294.t2.CDS1 | 16016355 | 16016693 |
| chr_2 | g6294 | g6294.t2 | exon | g6294.t2.exon2 | 16016840 | 16017128 |
| chr_2 | g6294 | g6294.t2 | TSS | g6294.t2 | 16017186 | 16017186 |
Sequences
>g6294.t2 Gene=g6294 Length=698
ATGGAAGTAGAAGTAGGAAATATTGTGCTACCAGGAAATATAGTGAAAGAAGCGGAATCA
CTTGCTAAAGAGAATAAGAAAGTAGTTCTTGGAAATGGTTTAAGATCAGACGAAAATGAA
AAAGTTGTAGTGTCGAAAAGCGGAATTCTTTGTAAAAGAAAGAACATTTTCTATGTGGAT
AGCTATCAAAAACGATATATTCCAGCCAAAAATGATACTGTAATAGGCATAGTACATTCA
AAAACATTAGATTTCTTTTGGGTTGACATTAATTGTTCAGAGCTTGCATGGCTTTTGAAG
GAGCTACAAAAAAGAATAGACCAGATATTAATATTGGTGATTTGATTTACTGTAAAGTTA
TGCAGTCAAATCCAGATTTAGAACCAGAACTAGTGTGTGTCGATTCAACAGGAAAGAAAG
GCAATTTAGGAGAATTAAAAGATGGACTAATGTTTAGCTGCACTATTAATCTAGTAAGAA
AGATACTCAATGAAAAATGTACACTCCTTCATTTACTTTCGAAAGAATGCCCTTACGAAA
TCGCTGCAGGAATAAACGGAAGAATATGGATTAATTCAAAAAATATCAACACTACGATAT
TATTAAGAAATACTATTTTAGAAGCTGAATATACTCCTTATCATCAAATGAAAAATCTAG
TTGATCGTTTTGCAAGTGAATTGACAGGAATAAATTAA
>g6294.t2 Gene=g6294 Length=112
MQSNPDLEPELVCVDSTGKKGNLGELKDGLMFSCTINLVRKILNEKCTLLHLLSKECPYE
IAAGINGRIWINSKNINTTILLRNTILEAEYTPYHQMKNLVDRFASELTGIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6294.t2 | Gene3D | G3DSA:3.30.1370.10 | - | 21 | 106 | 0 |
| 2 | g6294.t2 | PANTHER | PTHR21321:SF1 | EXOSOME COMPLEX COMPONENT RRP40 | 2 | 106 | 0 |
| 3 | g6294.t2 | PANTHER | PTHR21321 | PNAS-3 RELATED | 2 | 106 | 0 |
| 1 | g6294.t2 | Pfam | PF15985 | KH domain | 29 | 75 | 0 |
| 4 | g6294.t2 | SUPERFAMILY | SSF54791 | Eukaryotic type KH-domain (KH-domain type I) | 28 | 105 | 0 |
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: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.
