General information for g621.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 39S ribosomal protein L20, mitochondrial.
Parent gene
- The parent gene g621 is located on chr_3: 4537869..4538379 (+ 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 | g621 | g621.t1 | TSS | g621.t1 | 4537800 | 4537800 |
| chr_3 | g621 | g621.t1 | isoform | g621.t1 | 4537869 | 4538379 |
| chr_3 | g621 | g621.t1 | exon | g621.t1.exon1 | 4537869 | 4537955 |
| chr_3 | g621 | g621.t1 | cds | g621.t1.CDS1 | 4537869 | 4537955 |
| chr_3 | g621 | g621.t1 | exon | g621.t1.exon2 | 4538014 | 4538124 |
| chr_3 | g621 | g621.t1 | cds | g621.t1.CDS2 | 4538014 | 4538124 |
| chr_3 | g621 | g621.t1 | exon | g621.t1.exon3 | 4538185 | 4538379 |
| chr_3 | g621 | g621.t1 | cds | g621.t1.CDS3 | 4538185 | 4538379 |
| chr_3 | g621 | g621.t1 | TTS | g621.t1 | 4538428 | 4538428 |
Sequences
>g621.t1 Gene=g621 Length=393
ATGGTATTTCTTACTGCTGTAAACCTCATTAGATCACGAGGACCAGATGAATGGTGGAGA
AAGCGAAAAATCTTCAAATTAGCAGCTTATTTCTATGGACGAAGAAGAAATTGCTACAGT
CTTGCTATTCGTTCAGTTCATAGAGCATTAGTTTATGCAACAAAATCTCGACAAGAAAGA
AAGAGTGATTTAGCTGAGTTATGGAAACAAAGAATTACAGCTGGTGCTGCACAACATGGA
ATTGAATACTGGCAATTTATGGATGGATTACATAAAAATAATATTGAAATAAATAAAAAG
AACTTGGCTGATCTTGCCGCTTGGGAACCTGCATCTTTTGAATCGTTAGCTAAGATTTCT
AAAGATTTTGTTGAGAAAAATAGAAATAAATAA
>g621.t1 Gene=g621 Length=130
MVFLTAVNLIRSRGPDEWWRKRKIFKLAAYFYGRRRNCYSLAIRSVHRALVYATKSRQER
KSDLAELWKQRITAGAAQHGIEYWQFMDGLHKNNIEINKKNLADLAAWEPASFESLAKIS
KDFVEKNRNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g621.t1 | CDD | cd07026 | Ribosomal_L20 | 13 | 118 | 0 |
| 9 | g621.t1 | Gene3D | G3DSA:1.10.720.90 | - | 12 | 63 | 0 |
| 8 | g621.t1 | Gene3D | G3DSA:1.10.1900.20 | Ribosomal protein L20 | 66 | 123 | 0 |
| 2 | g621.t1 | PANTHER | PTHR10986:SF23 | LP04985P | 1 | 127 | 0 |
| 3 | g621.t1 | PANTHER | PTHR10986 | 39S RIBOSOMAL PROTEIN L20 | 1 | 127 | 0 |
| 4 | g621.t1 | PRINTS | PR00062 | Ribosomal protein L20 signature | 19 | 48 | 0 |
| 6 | g621.t1 | PRINTS | PR00062 | Ribosomal protein L20 signature | 49 | 78 | 0 |
| 5 | g621.t1 | PRINTS | PR00062 | Ribosomal protein L20 signature | 82 | 108 | 0 |
| 1 | g621.t1 | Pfam | PF00453 | Ribosomal protein L20 | 13 | 116 | 0 |
| 7 | g621.t1 | SUPERFAMILY | SSF74731 | Ribosomal protein L20 | 13 | 123 | 0 |
| 10 | g621.t1 | TIGRFAM | TIGR01032 | rplT_bact: ribosomal protein bL20 | 18 | 121 | 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 |
| GO:0019843 | rRNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K02887 (large subunit ribosomal protein L20)
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.
