General information for g6294.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g6294.t1 | 16016338 | 16016338 |
| chr_2 | g6294 | g6294.t1 | isoform | g6294.t1 | 16016355 | 16017128 |
| chr_2 | g6294 | g6294.t1 | exon | g6294.t1.exon1 | 16016355 | 16016776 |
| chr_2 | g6294 | g6294.t1 | cds | g6294.t1.CDS1 | 16016355 | 16016776 |
| chr_2 | g6294 | g6294.t1 | exon | g6294.t1.exon2 | 16016840 | 16017128 |
| chr_2 | g6294 | g6294.t1 | cds | g6294.t1.CDS2 | 16016840 | 16017128 |
| chr_2 | g6294 | g6294.t1 | TSS | g6294.t1 | 16017186 | 16017186 |
Sequences
>g6294.t1 Gene=g6294 Length=711
ATGGAAGTAGAAGTAGGAAATATTGTGCTACCAGGAAATATAGTGAAAGAAGCGGAATCA
CTTGCTAAAGAGAATAAGAAAGTAGTTCTTGGAAATGGTTTAAGATCAGACGAAAATGAA
AAAGTTGTAGTGTCGAAAAGCGGAATTCTTTGTAAAAGAAAGAACATTTTCTATGTGGAT
AGCTATCAAAAACGATATATTCCAGCCAAAAATGATACTGTAATAGGCATAGTACATTCA
AAAACATTAGATTTCTTTTGGGTTGACATTAATTGTTCAGAGCTTGCATCACTTCCTTAT
TTGGCTTTTGAAGGAGCTACAAAAAAGAATAGACCAGATATTAATATTGGTGATTTGATT
TACTGTAAAGTTATGCAGTCAAATCCAGATTTAGAACCAGAACTAGTGTGTGTCGATTCA
ACAGGAAAGAAAGGCAATTTAGGAGAATTAAAAGATGGACTAATGTTTAGCTGCACTATT
AATCTAGTAAGAAAGATACTCAATGAAAAATGTACACTCCTTCATTTACTTTCGAAAGAA
TGCCCTTACGAAATCGCTGCAGGAATAAACGGAAGAATATGGATTAATTCAAAAAATATC
AACACTACGATATTATTAAGAAATACTATTTTAGAAGCTGAATATACTCCTTATCATCAA
ATGAAAAATCTAGTTGATCGTTTTGCAAGTGAATTGACAGGAATAAATTAA
>g6294.t1 Gene=g6294 Length=236
MEVEVGNIVLPGNIVKEAESLAKENKKVVLGNGLRSDENEKVVVSKSGILCKRKNIFYVD
SYQKRYIPAKNDTVIGIVHSKTLDFFWVDINCSELASLPYLAFEGATKKNRPDINIGDLI
YCKVMQSNPDLEPELVCVDSTGKKGNLGELKDGLMFSCTINLVRKILNEKCTLLHLLSKE
CPYEIAAGINGRIWINSKNINTTILLRNTILEAEYTPYHQMKNLVDRFASELTGIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6294.t1 | CDD | cd05790 | S1_Rrp40 | 65 | 150 | 0 |
| 7 | g6294.t1 | Gene3D | G3DSA:2.40.50.100 | - | 4 | 67 | 0 |
| 8 | g6294.t1 | Gene3D | G3DSA:2.40.50.140 | - | 72 | 148 | 0 |
| 9 | g6294.t1 | Gene3D | G3DSA:3.30.1370.10 | - | 149 | 230 | 0 |
| 2 | g6294.t1 | PANTHER | PTHR21321:SF1 | EXOSOME COMPLEX COMPONENT RRP40 | 5 | 230 | 0 |
| 3 | g6294.t1 | PANTHER | PTHR21321 | PNAS-3 RELATED | 5 | 230 | 0 |
| 1 | g6294.t1 | Pfam | PF15985 | KH domain | 153 | 199 | 0 |
| 5 | g6294.t1 | SUPERFAMILY | SSF110324 | Ribosomal L27 protein-like | 2 | 64 | 0 |
| 6 | g6294.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 64 | 156 | 0 |
| 4 | g6294.t1 | SUPERFAMILY | SSF54791 | Eukaryotic type KH-domain (KH-domain type I) | 152 | 229 | 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 transcript has been annotated with K03681 (exosome complex component RRP40)
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.
