General information for g720.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L3, mitochondrial.
Parent gene
- The parent gene g720 is located on chr_3: 5502692..5504024 (+ 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 | g720 | g720.t3 | TSS | g720.t3 | 5501415 | 5501415 |
| chr_3 | g720 | g720.t3 | isoform | g720.t3 | 5501500 | 5502692 |
| chr_3 | g720 | g720.t3 | exon | g720.t3.exon1 | 5501500 | 5501558 |
| chr_3 | g720 | g720.t3 | cds | g720.t3.CDS1 | 5501500 | 5501558 |
| chr_3 | g720 | g720.t3 | exon | g720.t3.exon2 | 5501625 | 5501995 |
| chr_3 | g720 | g720.t3 | cds | g720.t3.CDS2 | 5501625 | 5501995 |
| chr_3 | g720 | g720.t3 | exon | g720.t3.exon3 | 5502086 | 5502215 |
| chr_3 | g720 | g720.t3 | cds | g720.t3.CDS3 | 5502086 | 5502215 |
| chr_3 | g720 | g720.t3 | exon | g720.t3.exon4 | 5502272 | 5502692 |
| chr_3 | g720 | g720.t3 | cds | g720.t3.CDS4 | 5502272 | 5502692 |
| chr_3 | g720 | g720.t3 | TTS | g720.t3 | 5502747 | 5502747 |
Sequences
>g720.t3 Gene=g720 Length=981
ATGTTTTTATCAAAAACCATAAAAACTGTTTTAGGTACTTCAATTATTAATGATGTTAGA
TACACACAAGTTTGTTTCCATCGATTTAAATTTATCCCTAAATTACGAGTACCTGAATGG
CATTTTAGAGTCGAAAGAAGAGCAAAGGACCGAGATGATAATCTGACGGAAAGAAATAAA
AGATTTATCAATGAAATGTCGAAAAAAGATCATGAAAAAGCATCTTTATTAAAAGTACCG
ACAGTTGAACCAAAAGAATGGAAGAAAGGAATGATTCGTTGTGGAATAGTTGCTAAAAAG
CTAGGCTATTATCCTCTTTGGACAAAAGATGGTACTCGAATTTGTACGACAGTTTTACAA
ATCATTGAAAATCATGTCATTAAATATGCACCACCTGGAGAATTCAATCCTACAATGAGA
AAACGTCTAGAAAGTGGTGTGATGCCAACACAAAGAATTACGCGTTTTATCATACATCCT
GATGCAGCACTTCCTATAGGCACATCAATCAATGCTCTTCATTATCGTGTTGGTGATTAT
GTTGATGTATTGGGTAAAACCGTTGATCAAGGCTGGCAAGGTGTCATTAAAAGATGGGGA
TTTAAAGGAGGACCAGCAACTCATGGAACTACTAAAAATCATAGACGTGGAGGATCTTTG
GCTTCAGGCATTAAAAGTAGAATTTGGAAAGGAAAGAAAATGCCTGGAAATATGGGGAAT
CGATGGAGAACTCTTCGTGGTTTAAAAATTTGGAGAATTAATAGAAAAGAAAATTGTATT
TGGGTGTCAGGTAGAGCAATCGCAGGAGCACCTGGAAGTTTAGTTTATATTTATGATACA
GTTTTACCACTTCGTCAACCTAAAGAACCTCTTCATTTTCCAACTTTTCTCGGTGATGAG
TCAAAATTACCTGAAGACATTTATGAAGAAACAATTCACAAATTTGGAGATTTGACGATA
ACATTTGAGCCCGAGAAATAA
>g720.t3 Gene=g720 Length=326
MFLSKTIKTVLGTSIINDVRYTQVCFHRFKFIPKLRVPEWHFRVERRAKDRDDNLTERNK
RFINEMSKKDHEKASLLKVPTVEPKEWKKGMIRCGIVAKKLGYYPLWTKDGTRICTTVLQ
IIENHVIKYAPPGEFNPTMRKRLESGVMPTQRITRFIIHPDAALPIGTSINALHYRVGDY
VDVLGKTVDQGWQGVIKRWGFKGGPATHGTTKNHRRGGSLASGIKSRIWKGKKMPGNMGN
RWRTLRGLKIWRINRKENCIWVSGRAIAGAPGSLVYIYDTVLPLRQPKEPLHFPTFLGDE
SKLPEDIYEETIHKFGDLTITFEPEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g720.t3 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 58 | 131 | 1.4e-05 |
| 5 | g720.t3 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 194 | 283 | 0.0e+00 |
| 2 | g720.t3 | PANTHER | PTHR11229 | 50S RIBOSOMAL PROTEIN L3 | 47 | 321 | 0.0e+00 |
| 3 | g720.t3 | PANTHER | PTHR11229:SF8 | 39S RIBOSOMAL PROTEIN L3, MITOCHONDRIAL | 47 | 321 | 0.0e+00 |
| 1 | g720.t3 | Pfam | PF00297 | Ribosomal protein L3 | 172 | 257 | 0.0e+00 |
| 4 | g720.t3 | SUPERFAMILY | SSF50447 | Translation proteins | 81 | 302 | 0.0e+00 |
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 K02906 (large subunit ribosomal protein L3)
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.
