General information for g2839.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 39S ribosomal protein L17, mitochondrial.
Parent gene
- The parent gene g2839 is located on chr_3: 20508007..20509267 (- 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 | g2839 | g2839.t1 | TTS | g2839.t1 | 20506490 | 20506490 |
| chr_3 | g2839 | g2839.t1 | isoform | g2839.t1 | 20507387 | 20508088 |
| chr_3 | g2839 | g2839.t1 | exon | g2839.t1.exon1 | 20507387 | 20507806 |
| chr_3 | g2839 | g2839.t1 | cds | g2839.t1.CDS1 | 20507387 | 20507806 |
| chr_3 | g2839 | g2839.t1 | exon | g2839.t1.exon2 | 20507867 | 20508088 |
| chr_3 | g2839 | g2839.t1 | cds | g2839.t1.CDS2 | 20507867 | 20508088 |
| chr_3 | g2839 | g2839.t1 | TSS | g2839.t1 | 20508190 | 20508190 |
Sequences
>g2839.t1 Gene=g2839 Length=642
ATGGTAGGAAAGCCATTAAAAAGTTTAGGCTATGCGGAAGTTACAAAGTTAATGTCAGAA
CTTAAAGTACCCGTTTTACCTCGTCATCGAAATTTAAGCTCGCCACTCGGTCCTGAAGGA
AGAATCAATAAATTGAGACAAACAGTGACTGCTTTAGTGAAATATGAGCGTATTGAGCTA
TTTCATAATCGTGCAGATGAAGCTCGTGGTTACGTCGAAAGATTAGTGTCAGATGCAAGA
AGATATGGAGACCAAAATAAAGAAATGATGGAAATGGCCAGTTATTGGCTACTAGAGAAA
CAACTTGTTCATAAATTATTTAAAGTAATTTGTCCACGATTTCATGATACATTTGATGGT
CCATTCACGACAGCTTATAATGCTCCTCGAAAATATCCAAGCGAAACAGAAAGAAAGCAA
TACTTTAAAAGAGTCGTTTTAGAGTTAAAAGGTCATCCATTTCCACCGCTTTTACCACAA
GCATCTTATCAAGGCAAATATCTTATTCATAATGTTCTTCTCGATGCCGCTATGAAAGAT
TATTATCAAGAAAAGAAATTAAATGCAATGCAGAACAAAAAAGAGGAAGTAACAGAATCA
GTTGATGAAGAAAAAGAACTTGATAATCAAATAAAAGAATAG
>g2839.t1 Gene=g2839 Length=213
MVGKPLKSLGYAEVTKLMSELKVPVLPRHRNLSSPLGPEGRINKLRQTVTALVKYERIEL
FHNRADEARGYVERLVSDARRYGDQNKEMMEMASYWLLEKQLVHKLFKVICPRFHDTFDG
PFTTAYNAPRKYPSETERKQYFKRVVLELKGHPFPPLLPQASYQGKYLIHNVLLDAAMKD
YYQEKKLNAMQNKKEEVTESVDEEKELDNQIKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2839.t1 | Coils | Coil | Coil | 187 | 210 | - |
| 6 | g2839.t1 | Gene3D | G3DSA:3.90.1030.10 | - | 38 | 151 | 3.2E-21 |
| 5 | g2839.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 213 | - |
| 2 | g2839.t1 | PANTHER | PTHR14413 | RIBOSOMAL PROTEIN L17 | 25 | 195 | 2.9E-19 |
| 3 | g2839.t1 | PANTHER | PTHR14413:SF16 | 39S RIBOSOMAL PROTEIN L17, MITOCHONDRIAL | 25 | 195 | 2.9E-19 |
| 1 | g2839.t1 | Pfam | PF01196 | Ribosomal protein L17 | 45 | 123 | 3.6E-11 |
| 4 | g2839.t1 | SUPERFAMILY | SSF64263 | Prokaryotic ribosomal protein L17 | 45 | 157 | 4.84E-21 |
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 transcript has been annotated with K02879 (large subunit ribosomal protein L17)
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.
