General information for g1710.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L18a.
Parent gene
- The parent gene g1710 is located on chr_3: 12637585..12638250 (- 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_3 | g1710 | g1710.t16 | TTS | g1710.t16 | 12637218 | 12637218 |
| chr_3 | g1710 | g1710.t16 | isoform | g1710.t16 | 12637362 | 12638250 |
| chr_3 | g1710 | g1710.t16 | exon | g1710.t16.exon1 | 12637362 | 12637520 |
| chr_3 | g1710 | g1710.t16 | cds | g1710.t16.CDS1 | 12637362 | 12637520 |
| chr_3 | g1710 | g1710.t16 | exon | g1710.t16.exon2 | 12637585 | 12637934 |
| chr_3 | g1710 | g1710.t16 | cds | g1710.t16.CDS2 | 12637585 | 12637872 |
| chr_3 | g1710 | g1710.t16 | exon | g1710.t16.exon3 | 12638236 | 12638250 |
| chr_3 | g1710 | g1710.t16 | TSS | g1710.t16 | 12638284 | 12638284 |
Sequences
>g1710.t16 Gene=g1710 Length=524
ATGAAAGCAAAAGGAAATATGAGATCATTGGCCGCAAATTGCCAAGTGAAAAGGATCCAA
ATCCACCTCTATTCAAAATGATAATCTTTGCACCGGATCACATCGTAGCCAAGTCTCGTT
TCTGGTATTTCTTGCGTCAATTGCGCAAATTCAAGAAGGCCACCGGTGAGATCGTGAGTG
TTAAGCGCAAATATGAGAAAACTCCACTCAAGATCAAGAATTTCGGTATCTGGCTTCGTT
ATGACTCGCGTTCAGGAACACATAACATGTATCGCGAATACCGTGATTTGACAATTGGTG
GTGCAGTTACACAATGTTATTCCGATATGGCTTCACGCCATCGTGCTCGCGCTCACTCAA
TTCAAATTATCAAAATTGAGAAAGTTGCAGCAATCAAGACTCGTCGTGCACACATCAAGC
AATTCCACGATTCAAAGATCAGATTCCCATTGGTGCAGCGATATCATCACAAACGCTATC
GTCAACTGTTCTCAATTGCTCGCCCAACTACACACTTCAACTAA
>g1710.t16 Gene=g1710 Length=148
MIIFAPDHIVAKSRFWYFLRQLRKFKKATGEIVSVKRKYEKTPLKIKNFGIWLRYDSRSG
THNMYREYRDLTIGGAVTQCYSDMASRHRARAHSIQIIKIEKVAAIKTRRAHIKQFHDSK
IRFPLVQRYHHKRYRQLFSIARPTTHFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1710.t16 | Gene3D | G3DSA:3.10.20.10 | - | 1 | 43 | 0 |
| 5 | g1710.t16 | Gene3D | G3DSA:3.10.20.10 | - | 44 | 119 | 0 |
| 2 | g1710.t16 | PANTHER | PTHR10052 | 60S RIBOSOMAL PROTEIN L18A | 1 | 147 | 0 |
| 3 | g1710.t16 | PANTHER | PTHR10052:SF50 | 60S RIBOSOMAL PROTEIN L18A | 1 | 147 | 0 |
| 7 | g1710.t16 | PIRSF | PIRSF002190 | Ribosomal_L18a | 1 | 147 | 0 |
| 1 | g1710.t16 | Pfam | PF01775 | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A | 1 | 101 | 0 |
| 4 | g1710.t16 | SUPERFAMILY | SSF160374 | RplX-like | 43 | 118 | 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: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.
