General information for g5231.t40
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.t40 | TTS | g5231.t40 | 7931500 | 7931500 |
| chr_2 | g5231 | g5231.t40 | isoform | g5231.t40 | 7931553 | 7939140 |
| chr_2 | g5231 | g5231.t40 | exon | g5231.t40.exon1 | 7931553 | 7931881 |
| chr_2 | g5231 | g5231.t40 | cds | g5231.t40.CDS1 | 7931553 | 7931881 |
| chr_2 | g5231 | g5231.t40 | exon | g5231.t40.exon2 | 7931953 | 7932196 |
| chr_2 | g5231 | g5231.t40 | cds | g5231.t40.CDS2 | 7931953 | 7932193 |
| chr_2 | g5231 | g5231.t40 | exon | g5231.t40.exon3 | 7932418 | 7932447 |
| chr_2 | g5231 | g5231.t40 | TSS | g5231.t40 | 7932458 | 7932458 |
| chr_2 | g5231 | g5231.t40 | exon | g5231.t40.exon4 | 7939046 | 7939140 |
Sequences
>g5231.t40 Gene=g5231 Length=698
TTTCGGAATCATCGTGATCATCTTCAAAATTATAACTTGAAGGTCGCAAGGAACTTGACA
AATTGTCAGAAAAGTCATCGATGATTCTTTGATGCGATCTCTGTGAAGAGCATTAATTTT
TCGAGATCATGAGAACTATCAACAGCAATCAAGTTGTTAAGCTTCCAAAAGGCGTTGGCG
CAAAAGTCAATGCTCGCGTTATTACAATTCGAGGGCCAAGAGGCAAATTGACTCGCGATT
TCCGTCACTTAGCAATGGATATTCGTATGATCAATCGCAAGAAGATTATGGTTGAGAAGT
GGTTCGGAGCTAAAAAAGAAATTGCTGCTGTAAGAACTGTTTGCAGTCATATCGAAAATA
TGATCAAGGTTACAAAGGGATTCCAATATAAAATGAGAGCTGTACATGCGCATTTTCCCA
TCAACTGTGTTGTGTCAGAAAATAATACTGTTATTGAAATCCGTAACTTCTTGGGTGAAA
AGCACATTCGTAAAGTAACAATGAAACCAGGTGTTACAGTTGTCAACTCAGCTAAGCAAA
AGGATGAATTGATCCTTGAAGGAAATGATATCGAAGCAGTTTCACTATCTGCTGCTCTTA
TTCAACAATCAACAACAGTTAAAAATAAGGATATTCGTAAATTCCTTGACGGTTTGTATG
TCTCAGAGAAGACTACTGTGGTACAAGAAGAAGAATAA
>g5231.t40 Gene=g5231 Length=189
MRTINSNQVVKLPKGVGAKVNARVITIRGPRGKLTRDFRHLAMDIRMINRKKIMVEKWFG
AKKEIAAVRTVCSHIENMIKVTKGFQYKMRAVHAHFPINCVVSENNTVIEIRNFLGEKHI
RKVTMKPGVTVVNSAKQKDELILEGNDIEAVSLSAALIQQSTTVKNKDIRKFLDGLYVSE
KTTVVQEEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5231.t40 | Gene3D | G3DSA:3.90.930.12 | - | 1 | 84 | 2.5E-30 |
| 9 | g5231.t40 | Gene3D | G3DSA:3.90.930.12 | - | 85 | 189 | 5.0E-45 |
| 3 | g5231.t40 | PANTHER | PTHR11655:SF16 | 60S RIBOSOMAL PROTEIN L9-RELATED | 1 | 187 | 5.8E-78 |
| 4 | g5231.t40 | PANTHER | PTHR11655 | 60S/50S RIBOSOMAL PROTEIN L6/L9 | 1 | 187 | 5.8E-78 |
| 10 | g5231.t40 | PIRSF | PIRSF002162 | RPL6p_RPL6a_RPL9e_RPL9o | 1 | 183 | 1.1E-33 |
| 1 | g5231.t40 | Pfam | PF00347 | Ribosomal protein L6 | 13 | 81 | 1.2E-12 |
| 2 | g5231.t40 | Pfam | PF00347 | Ribosomal protein L6 | 96 | 175 | 4.2E-16 |
| 7 | g5231.t40 | ProSitePatterns | PS00700 | Ribosomal protein L6 signature 2. | 160 | 181 | - |
| 5 | g5231.t40 | SUPERFAMILY | SSF56053 | Ribosomal protein L6 | 1 | 80 | 1.37E-18 |
| 6 | g5231.t40 | SUPERFAMILY | SSF56053 | Ribosomal protein L6 | 85 | 181 | 1.92E-28 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5231/g5231.t40; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5231.t40.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 transcript has been annotated with K02940 (large subunit ribosomal protein L9e)
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.
