General information for g1342.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L11, mitochondrial.
Parent gene
- The parent gene g1342 is located on chr_3: 9941652..9942739 (- 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 | g1342 | g1342.t1 | TTS | g1342.t1 | 9940883 | 9940883 |
| chr_3 | g1342 | g1342.t1 | isoform | g1342.t1 | 9940945 | 9941652 |
| chr_3 | g1342 | g1342.t1 | exon | g1342.t1.exon1 | 9940945 | 9941316 |
| chr_3 | g1342 | g1342.t1 | cds | g1342.t1.CDS1 | 9940945 | 9941316 |
| chr_3 | g1342 | g1342.t1 | exon | g1342.t1.exon2 | 9941373 | 9941488 |
| chr_3 | g1342 | g1342.t1 | cds | g1342.t1.CDS2 | 9941373 | 9941488 |
| chr_3 | g1342 | g1342.t1 | exon | g1342.t1.exon3 | 9941556 | 9941652 |
| chr_3 | g1342 | g1342.t1 | cds | g1342.t1.CDS3 | 9941556 | 9941652 |
| chr_3 | g1342 | g1342.t1 | TSS | g1342.t1 | 9941696 | 9941696 |
Sequences
>g1342.t1 Gene=g1342 Length=585
ATGTCGAAAGCGGTGAGAAGAGTAGTAAAGAAAGCTGTAGAGAAAATTAATCATTCTGGA
CCGCTTCGAACAGATATTCCAGCACAAATGGCAGTTGCTGCTCCTCCTTTAGGTCCACAA
CTTGGTCAACGAGGAATTAATATTGCTGCATTTTGCAAAGATTTCAATGAAAAGACTAAA
CATATTAAAGAAGGAACACCATTACCAACTAGAGTCTATGCAAAACCTGATAAAACTTAT
GAGCTCATCATACACTCGCCACCAGCGTCATTTTTATTAAAACAAGCAGCTGGCATTCAA
AGAGGAACAATGTTTCCTGGAAAGGAAATTGCCGGCAAAATCACATTAAAACATCTTTAT
GAAATTGCTGCAATTAAAATTCAAGATCCACCAAATGCACTTTTAACAATGGAACAAATG
TGCAATCTTTTAATTGGAACAGCTCGTACATGTGGCATTGAAATTGTGAAAGAATTAGAT
GCAAATGAATATGGAAAATTTTTAGAAGAGAGAAAAGTAATTGTTGAACAACAGAAGAAA
GAACTACAAGAAAAGAAAGAAGCCAAGATGTTGAGAACAGCATAG
>g1342.t1 Gene=g1342 Length=194
MSKAVRRVVKKAVEKINHSGPLRTDIPAQMAVAAPPLGPQLGQRGINIAAFCKDFNEKTK
HIKEGTPLPTRVYAKPDKTYELIIHSPPASFLLKQAAGIQRGTMFPGKEIAGKITLKHLY
EIAAIKIQDPPNALLTMEQMCNLLIGTARTCGIEIVKELDANEYGKFLEERKVIVEQQKK
ELQEKKEAKMLRTA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1342.t1 | CDD | cd00349 | Ribosomal_L11 | 26 | 155 | 3.32125E-53 |
| 10 | g1342.t1 | Coils | Coil | Coil | 165 | 194 | - |
| 8 | g1342.t1 | Gene3D | G3DSA:3.30.1550.10 | Ribosomal protein L11 | 19 | 84 | 5.4E-27 |
| 9 | g1342.t1 | Gene3D | G3DSA:1.10.10.250 | - | 86 | 157 | 6.2E-27 |
| 5 | g1342.t1 | Hamap | MF_00736 | 50S ribosomal protein L11 [rplK]. | 18 | 157 | 23.706289 |
| 3 | g1342.t1 | PANTHER | PTHR11661:SF1 | 39S RIBOSOMAL PROTEIN L11, MITOCHONDRIAL | 13 | 164 | 1.1E-48 |
| 4 | g1342.t1 | PANTHER | PTHR11661 | 60S RIBOSOMAL PROTEIN L12 | 13 | 164 | 1.1E-48 |
| 2 | g1342.t1 | Pfam | PF03946 | Ribosomal protein L11, N-terminal domain | 20 | 80 | 7.2E-22 |
| 1 | g1342.t1 | Pfam | PF00298 | Ribosomal protein L11, RNA binding domain | 86 | 155 | 3.5E-23 |
| 12 | g1342.t1 | SMART | SM00649 | rl11c | 22 | 156 | 8.7E-59 |
| 6 | g1342.t1 | SUPERFAMILY | SSF54747 | Ribosomal L11/L12e N-terminal domain | 21 | 85 | 5.23E-22 |
| 7 | g1342.t1 | SUPERFAMILY | SSF46906 | Ribosomal protein L11, C-terminal domain | 82 | 155 | 1.01E-18 |
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 K02867 (large subunit ribosomal protein L11)
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.
