General information for g11817.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L17.
Parent gene
- The parent gene g11817 is located on chr_1: 18567996..18568461 (- 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_1 | g11817 | g11817.t1 | TTS | g11817.t1 | 18567884 | 18567884 |
| chr_1 | g11817 | g11817.t1 | isoform | g11817.t1 | 18567996 | 18568461 |
| chr_1 | g11817 | g11817.t1 | exon | g11817.t1.exon1 | 18567996 | 18568205 |
| chr_1 | g11817 | g11817.t1 | cds | g11817.t1.CDS1 | 18567996 | 18568205 |
| chr_1 | g11817 | g11817.t1 | exon | g11817.t1.exon2 | 18568261 | 18568461 |
| chr_1 | g11817 | g11817.t1 | cds | g11817.t1.CDS2 | 18568261 | 18568461 |
| chr_1 | g11817 | g11817.t1 | TSS | g11817.t1 | 18569439 | 18569439 |
Sequences
>g11817.t1 Gene=g11817 Length=411
ATGGAGCAGAAAGAATGTGTTCCATTCCGTCGTTTCAATGGTGCTGTTGGTCGTTGCGCT
CAAGCCAAACAGTGGGGAACCTCAATTGGTCGTTGGCCAAAAAAATCTGCCGATTTTCTT
CTTCAATTGTTGAAAAATGCAGAAGCTAATGCCGATTATAAAGGTTTAAATACTGATAAC
TTGGTTATTGATCATATTCAGGTCAATCGTGCTCCATGCTTGCGCCGTCGTACATACCGT
GCTCATGGTCGTATTAATCCATACATGTCATCACCATGCCACATTGAGCTAACACTTACA
GAAAAGGAAAAAGTTGCTCCATCAAAACCAACTGATGAAGAGCCTGAGAAGAAAAAAGTG
TCAAAGAAAAAGCTCCAAAAACAAAAAGAAAAGATGATGCGTGATGAATAA
>g11817.t1 Gene=g11817 Length=136
MEQKECVPFRRFNGAVGRCAQAKQWGTSIGRWPKKSADFLLQLLKNAEANADYKGLNTDN
LVIDHIQVNRAPCLRRRTYRAHGRINPYMSSPCHIELTLTEKEKVAPSKPTDEEPEKKKV
SKKKLQKQKEKMMRDE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11817.t1 | CDD | cd00336 | Ribosomal_L22 | 33 | 99 | 1.05579E-29 |
| 6 | g11817.t1 | Coils | Coil | Coil | 122 | 136 | - |
| 5 | g11817.t1 | Gene3D | G3DSA:3.90.470.10 | Ribosomal Protein L22; Chain A | 1 | 136 | 4.9E-58 |
| 9 | g11817.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 99 | 136 | - |
| 10 | g11817.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 99 | 121 | - |
| 2 | g11817.t1 | PANTHER | PTHR11593:SF28 | - | 3 | 131 | 4.7E-63 |
| 3 | g11817.t1 | PANTHER | PTHR11593 | 60S RIBOSOMAL PROTEIN L17 | 3 | 131 | 4.7E-63 |
| 1 | g11817.t1 | Pfam | PF00237 | Ribosomal protein L22p/L17e | 33 | 100 | 3.7E-27 |
| 8 | g11817.t1 | ProSitePatterns | PS00464 | Ribosomal protein L22 signature. | 75 | 99 | - |
| 4 | g11817.t1 | SUPERFAMILY | SSF54843 | Ribosomal protein L22 | 2 | 102 | 1.83E-40 |
| 11 | g11817.t1 | TIGRFAM | TIGR01038 | uL22_arch_euk: ribosomal protein uL22 | 2 | 102 | 2.3E-42 |
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:0015934 | large ribosomal subunit | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02880 (large subunit ribosomal protein L17e)
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.
