General information for g14134.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Exosome complex component CSL4.
Parent gene
- The parent gene g14134 is located on chr_1: 34849792..34850063 (+ 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 | g14134 | g14134.t1 | TSS | g14134.t1 | 34849321 | 34849321 |
| chr_1 | g14134 | g14134.t1 | isoform | g14134.t1 | 34849386 | 34850056 |
| chr_1 | g14134 | g14134.t1 | exon | g14134.t1.exon1 | 34849386 | 34849526 |
| chr_1 | g14134 | g14134.t1 | cds | g14134.t1.CDS1 | 34849386 | 34849526 |
| chr_1 | g14134 | g14134.t1 | exon | g14134.t1.exon2 | 34849580 | 34850056 |
| chr_1 | g14134 | g14134.t1 | cds | g14134.t1.CDS2 | 34849580 | 34850056 |
| chr_1 | g14134 | g14134.t1 | TTS | g14134.t1 | 34850076 | 34850076 |
Sequences
>g14134.t1 Gene=g14134 Length=618
ATGGAAGAAATTGCTGCTTTTCCTGGACAAAGAATCTGTGTAGCTAACGAAAATACAATA
TCAAGCACTGGAACTTATGAGAGATTAGGCTATATTTATTCTTCATTAGCTGGAATCGTA
GAAACTAAAGATGAAGACAAAAATAAAATAATCAGTGTAAGAGCTTCTGGACAAAAAACT
GTGCTTCCTATGGTGGGTGATGTAGTAACAGCTCGAGTAGAAATAGTTAATCAGCGTTTT
GCGAAATGTCAAATTATCTGCATAAACGATATTTTATTGAATAGACCTCTTAGAGGGATT
TTACGAAAAGAAGACGTTAGAGCAACAGATATTGATCGAGTGGAAATGTATAAAAACTTT
CGACCAAATGATATAATTTTAGCAAAAATAATACCACAAATTGAACTTCATACATACAGT
TTAAGTACAGCAGAGAATGAATTAGGTGTTGTTATAGCAAATCCTCGTTCAATAATCACA
TCATCTGGAAAATATTTCACAAACCCGATGGTACCAATTTCATGGGCAAAAATGAAATGT
CCTTTAACGGGCGTTGAAGAACCAAGAAAAGTGGCAAAAATCATGTCAGAAGACTCATTA
GTAAAAAGAGAACAATAA
>g14134.t1 Gene=g14134 Length=205
MEEIAAFPGQRICVANENTISSTGTYERLGYIYSSLAGIVETKDEDKNKIISVRASGQKT
VLPMVGDVVTARVEIVNQRFAKCQIICINDILLNRPLRGILRKEDVRATDIDRVEMYKNF
RPNDIILAKIIPQIELHTYSLSTAENELGVVIANPRSIITSSGKYFTNPMVPISWAKMKC
PLTGVEEPRKVAKIMSEDSLVKREQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g14134.t1 | Gene3D | G3DSA:2.40.50.100 | - | 5 | 53 | 0e+00 |
| 7 | g14134.t1 | Gene3D | G3DSA:2.40.50.140 | - | 55 | 200 | 0e+00 |
| 3 | g14134.t1 | PANTHER | PTHR12686 | 3’-5’ EXORIBONUCLEASE CSL4-RELATED | 6 | 195 | 0e+00 |
| 1 | g14134.t1 | Pfam | PF14382 | Exosome complex exonuclease RRP4 N-terminal region | 7 | 42 | 0e+00 |
| 2 | g14134.t1 | Pfam | PF10447 | Exosome component EXOSC1/CSL4 | 94 | 131 | 2e-07 |
| 4 | g14134.t1 | SUPERFAMILY | SSF110324 | Ribosomal L27 protein-like | 6 | 48 | 0e+00 |
| 5 | g14134.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 63 | 191 | 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:0006396 | RNA processing | BP |
| GO:0003723 | RNA binding | MF |
| GO:0000178 | exosome (RNase complex) | CC |
KEGG
Orthology
- This transcript has been annotated with K07573 (exosome complex component CSL4)
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.
