General information for g8374.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L13.
Parent gene
- The parent gene g8374 is located on chr_2: 30066515..30072851 (- 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_2 | g8374 | g8374.t16 | isoform | g8374.t16 | 30066429 | 30067691 |
| chr_2 | g8374 | g8374.t16 | exon | g8374.t16.exon1 | 30066429 | 30066931 |
| chr_2 | g8374 | g8374.t16 | TTS | g8374.t16 | 30066432 | 30066432 |
| chr_2 | g8374 | g8374.t16 | cds | g8374.t16.CDS1 | 30066515 | 30066931 |
| chr_2 | g8374 | g8374.t16 | exon | g8374.t16.exon2 | 30066992 | 30067123 |
| chr_2 | g8374 | g8374.t16 | cds | g8374.t16.CDS2 | 30066992 | 30067123 |
| chr_2 | g8374 | g8374.t16 | exon | g8374.t16.exon3 | 30067172 | 30067245 |
| chr_2 | g8374 | g8374.t16 | cds | g8374.t16.CDS3 | 30067172 | 30067228 |
| chr_2 | g8374 | g8374.t16 | exon | g8374.t16.exon4 | 30067659 | 30067691 |
| chr_2 | g8374 | g8374.t16 | TSS | g8374.t16 | 30067694 | 30067694 |
Sequences
>g8374.t16 Gene=g8374 Length=742
TTTCTCATAATTTTCTTGTCCAACGAGTTGAAAATTAACCCTAACTCAAAATGAAGGGCA
ATCAAATGATTCCAAATGCCCACTTTCACAAGTGGTGGCAACGATTTAATCGTATTGCAA
AAGCTAAAGCAGCTTTCCCAAGACCTGCATCAAAATTGCGACCAATTGTAAGATGTCCAT
CAATCCGTTATTCAACAAAACTCAGAATGGGACGTGGATTTTCATTGGCTGAATTGAAGG
CTGCTGGTCTCACAGCTGGTTTTGCCCGATCTGTGGGTATTTCAGTTGATCGTCGTCGTC
GCAACAAGTCGGTTGAATCAAGACAACAGAATGTTCAACGCTTGAAGGAATATCAAAATA
AACTCATCCTCTTCCCAGTTCATGAAAATAAGAAGAACTTGAAATTGCGAAAGGGTGAAG
CAACAGAAGAAGAACGTAAATTGGCTACACAATTGACAGGTCCTATAATGCCACTCGTTA
AACCTAAACCAACCATTGAATTCCGCGCAATTAAGGAAGATGAAAAGAAGTTCTCTGCCT
TCAATGCTATCCACTGCGCTCGTGTTGCTGCTCGTACAGCTGGCAAACGCGCAAAGGCTG
CTAAAGATGCTGCAGATGCCGCAGAAAATGCACCAGGAGCCAAGAAGGATAAATAAGCAA
AAGGAATCATTTAATTTGTATAAGCTTATATTATCATAAACATCCAAGAAATAAATGATA
TGATACTTGTTTTTCCAACAAA
>g8374.t16 Gene=g8374 Length=201
MKGNQMIPNAHFHKWWQRFNRIAKAKAAFPRPASKLRPIVRCPSIRYSTKLRMGRGFSLA
ELKAAGLTAGFARSVGISVDRRRRNKSVESRQQNVQRLKEYQNKLILFPVHENKKNLKLR
KGEATEEERKLATQLTGPIMPLVKPKPTIEFRAIKEDEKKFSAFNAIHCARVAARTAGKR
AKAAKDAADAAENAPGAKKDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g8374.t16 | Hamap | MF_00499 | 50S ribosomal protein L13e [rpl13e]. | 27 | 110 | 21.980545 |
| 6 | g8374.t16 | MobiDBLite | mobidb-lite | consensus disorder prediction | 178 | 201 | - |
| 5 | g8374.t16 | MobiDBLite | mobidb-lite | consensus disorder prediction | 179 | 201 | - |
| 2 | g8374.t16 | PANTHER | PTHR11722 | 60S RIBOSOMAL PROTEIN L13 | 2 | 191 | 3.5E-59 |
| 1 | g8374.t16 | Pfam | PF01294 | Ribosomal protein L13e | 8 | 171 | 5.5E-53 |
| 4 | g8374.t16 | ProSitePatterns | PS01104 | Ribosomal protein L13e signature. | 52 | 66 | - |
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 K02873 (large subunit ribosomal protein L13e)
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.
