General information for g5932.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L31.
Parent gene
- The parent gene g5932 is located on chr_2: 12895340..12895485 (+ 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 | g5932 | g5932.t8 | isoform | g5932.t8 | 12894641 | 12895485 |
| chr_2 | g5932 | g5932.t8 | exon | g5932.t8.exon1 | 12894641 | 12894681 |
| chr_2 | g5932 | g5932.t8 | TSS | g5932.t8 | 12895044 | 12895044 |
| chr_2 | g5932 | g5932.t8 | exon | g5932.t8.exon2 | 12895060 | 12895274 |
| chr_2 | g5932 | g5932.t8 | cds | g5932.t8.CDS1 | 12895210 | 12895274 |
| chr_2 | g5932 | g5932.t8 | exon | g5932.t8.exon3 | 12895338 | 12895485 |
| chr_2 | g5932 | g5932.t8 | cds | g5932.t8.CDS2 | 12895338 | 12895485 |
| chr_2 | g5932 | g5932.t8 | TTS | g5932.t8 | 12895626 | 12895626 |
Sequences
>g5932.t8 Gene=g5932 Length=404
AACTCTTTCTTTTTTCTCTAACAAACTCACACGTTTGGTATGGTAAAACAGAAAAGCGTA
CCAAATCGGCAATCAATGAAGTTGTGACACGAGAGTGCACAATTCATCTGAATAAGCGAC
TCCACAAAGTTGGTTTTAAAAAACGTTCACCAAGAGCAGTTAAGATCATTCGTAAATTTG
CTGAAAAGGAAATGGGAACAAAAGATGTGAGAATTGATACCCGTCTTAATAAAGCAATTT
GGTCTCGCGGTATCAGAAATCCACCTTTCCGCATTCGTGTTCGACTTGCTCGCCGCCGTA
ATGATGATGAAGATTCACCTAACAAGCTTTATACTTTGGTCACATACGTCCCAGTGGAAA
GCTTCAAAGAACTCCAAACAGAAAATGTTGAATCAGAAGATTAA
>g5932.t8 Gene=g5932 Length=70
MGTKDVRIDTRLNKAIWSRGIRNPPFRIRVRLARRRNDDEDSPNKLYTLVTYVPVESFKE
LQTENVESED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5932.t8 | Gene3D | G3DSA:3.10.440.10 | - | 1 | 69 | 4.4E-34 |
| 2 | g5932.t8 | PANTHER | PTHR10956:SF4 | 60S RIBOSOMAL PROTEIN L31 | 1 | 68 | 5.9E-31 |
| 3 | g5932.t8 | PANTHER | PTHR10956 | 60S RIBOSOMAL PROTEIN L31 | 1 | 68 | 5.9E-31 |
| 1 | g5932.t8 | Pfam | PF01198 | Ribosomal protein L31e | 1 | 44 | 1.3E-21 |
| 6 | g5932.t8 | ProSitePatterns | PS01144 | Ribosomal protein L31e signature. | 6 | 20 | - |
| 5 | g5932.t8 | SMART | SM01380 | Ribosomal_L31e_2 | 1 | 45 | 1.8E-11 |
| 4 | g5932.t8 | SUPERFAMILY | SSF54575 | Ribosomal protein L31e | 1 | 45 | 1.03E-17 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5932/g5932.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5932.t8.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005840 | ribosome | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
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. There were no conditions that were differentially expressed