General information for g5231.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L9.
Parent gene
- The parent gene g5231 is located on chr_2: 7932013..7939140 (- 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 | g5231 | g5231.t16 | TTS | g5231.t16 | 7931500 | 7931500 |
| chr_2 | g5231 | g5231.t16 | isoform | g5231.t16 | 7931553 | 7932458 |
| chr_2 | g5231 | g5231.t16 | exon | g5231.t16.exon1 | 7931553 | 7931884 |
| chr_2 | g5231 | g5231.t16 | cds | g5231.t16.CDS1 | 7931553 | 7931884 |
| chr_2 | g5231 | g5231.t16 | exon | g5231.t16.exon2 | 7931953 | 7932188 |
| chr_2 | g5231 | g5231.t16 | cds | g5231.t16.CDS2 | 7931953 | 7932067 |
| chr_2 | g5231 | g5231.t16 | exon | g5231.t16.exon3 | 7932418 | 7932458 |
| chr_2 | g5231 | g5231.t16 | TSS | g5231.t16 | 7932458 | 7932458 |
Sequences
>g5231.t16 Gene=g5231 Length=609
CTTTTTTATTCGATCTCTGTGAAGAGCATTAATTTTTCGAGAACTATCAACAGCAATCAA
GTTGTTAAGCTTCCAAAAGGCGTTGGCGCAAAAGTCAATGCTCGCGTTATTACAATTCGA
GGGCCAAGAGGCAAATTGACTCGCGATTTCCGTCACTTAGCAATGGATATTCGTATGATC
AATCGCAAGAAGATTATGGTTGAGAAGTGGTTCGGAGCTAAAAAAGAAATTGCTGCTGTA
AGAACTGTTTGCAGTCATATCGAAAATATGATCAAGGGAGTTACAAAGGGATTCCAATAT
AAAATGAGAGCTGTACATGCGCATTTTCCCATCAACTGTGTTGTGTCAGAAAATAATACT
GTTATTGAAATCCGTAACTTCTTGGGTGAAAAGCACATTCGTAAAGTAACAATGAAACCA
GGTGTTACAGTTGTCAACTCAGCTAAGCAAAAGGATGAATTGATCCTTGAAGGAAATGAT
ATCGAAGCAGTTTCACTATCTGCTGCTCTTATTCAACAATCAACAACAGTTAAAAATAAG
GATATTCGTAAATTCCTTGACGGTTTGTATGTCTCAGAGAAGACTACTGTGGTACAAGAA
GAAGAATAA
>g5231.t16 Gene=g5231 Length=148
MDIRMINRKKIMVEKWFGAKKEIAAVRTVCSHIENMIKGVTKGFQYKMRAVHAHFPINCV
VSENNTVIEIRNFLGEKHIRKVTMKPGVTVVNSAKQKDELILEGNDIEAVSLSAALIQQS
TTVKNKDIRKFLDGLYVSEKTTVVQEEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5231.t16 | Gene3D | G3DSA:3.90.930.12 | - | 1 | 45 | 3.1E-16 |
| 9 | g5231.t16 | Gene3D | G3DSA:3.90.930.12 | - | 46 | 148 | 2.5E-45 |
| 3 | g5231.t16 | PANTHER | PTHR11655:SF26 | 60S RIBOSOMAL PROTEIN L9 | 7 | 148 | 3.9E-66 |
| 4 | g5231.t16 | PANTHER | PTHR11655 | 60S/50S RIBOSOMAL PROTEIN L6/L9 | 7 | 148 | 3.9E-66 |
| 10 | g5231.t16 | PIRSF | PIRSF002162 | RPL6p_RPL6a_RPL9e_RPL9o | 2 | 142 | 7.9E-30 |
| 2 | g5231.t16 | Pfam | PF00347 | Ribosomal protein L6 | 7 | 43 | 7.6E-8 |
| 1 | g5231.t16 | Pfam | PF00347 | Ribosomal protein L6 | 55 | 134 | 2.3E-16 |
| 7 | g5231.t16 | ProSitePatterns | PS00700 | Ribosomal protein L6 signature 2. | 119 | 140 | - |
| 5 | g5231.t16 | SUPERFAMILY | SSF56053 | Ribosomal protein L6 | 6 | 43 | 9.46E-9 |
| 6 | g5231.t16 | SUPERFAMILY | SSF56053 | Ribosomal protein L6 | 44 | 140 | 9.92E-29 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5231/g5231.t16; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5231.t16.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 |
| GO:0019843 | rRNA binding | 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