General information for g8374.t4
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.t4 | isoform | g8374.t4 | 30066429 | 30067228 |
| chr_2 | g8374 | g8374.t4 | exon | g8374.t4.exon1 | 30066429 | 30066934 |
| chr_2 | g8374 | g8374.t4 | TTS | g8374.t4 | 30066432 | 30066432 |
| chr_2 | g8374 | g8374.t4 | cds | g8374.t4.CDS1 | 30066515 | 30066934 |
| chr_2 | g8374 | g8374.t4 | exon | g8374.t4.exon2 | 30066992 | 30067228 |
| chr_2 | g8374 | g8374.t4 | cds | g8374.t4.CDS2 | 30066992 | 30067228 |
| chr_2 | g8374 | g8374.t4 | TSS | g8374.t4 | 30067694 | 30067694 |
Sequences
>g8374.t4 Gene=g8374 Length=743
ATGAAGGGCAATCAAATGATTCCAAATGCCCACTTTCACAAGTGGTGGCAACGATTTGTG
AGAACTTGGTTCAATCAACCAGCCAGAAAATATCGTCGTCGTCAGAATCGTATTGCAAAA
GCTAAAGCAGCTTTCCCAAGACCTGCATCAAAATTGCGACCAATTGTAAGATGTCCATCA
ATCCGTTATTCAACAAAACTCAGAATGGGACGTGGATTTTCATTGGCTGAATTGAAGAAG
GCTGCTGGTCTCACAGCTGGTTTTGCCCGATCTGTGGGTATTTCAGTTGATCGTCGTCGT
CGCAACAAGTCGGTTGAATCAAGACAACAGAATGTTCAACGCTTGAAGGAATATCAAAAT
AAACTCATCCTCTTCCCAGTTCATGAAAATAAGAAGAACTTGAAATTGCGAAAGGGTGAA
GCAACAGAAGAAGAACGTAAATTGGCTACACAATTGACAGGTCCTATAATGCCACTCGTT
AAACCTAAACCAACCATTGAATTCCGCGCAATTAAGGAAGATGAAAAGAAGTTCTCTGCC
TTCAATGCTATCCACTGCGCTCGTGTTGCTGCTCGTACAGCTGGCAAACGCGCAAAGGCT
GCTAAAGATGCTGCAGATGCCGCAGAAAATGCACCAGGAGCCAAGAAGGATAAATAAGCA
AAAGGAATCATTTAATTTGTATAAGCTTATATTATCATAAACATCCAAGAAATAAATGAT
ATGATACTTGTTTTTCCAACAAA
>g8374.t4 Gene=g8374 Length=218
MKGNQMIPNAHFHKWWQRFVRTWFNQPARKYRRRQNRIAKAKAAFPRPASKLRPIVRCPS
IRYSTKLRMGRGFSLAELKKAAGLTAGFARSVGISVDRRRRNKSVESRQQNVQRLKEYQN
KLILFPVHENKKNLKLRKGEATEEERKLATQLTGPIMPLVKPKPTIEFRAIKEDEKKFSA
FNAIHCARVAARTAGKRAKAAKDAADAAENAPGAKKDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g8374.t4 | Hamap | MF_00499 | 50S ribosomal protein L13e [rpl13e]. | 43 | 127 | 19.454041 |
| 5 | g8374.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 218 | - |
| 4 | g8374.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 196 | 218 | - |
| 2 | g8374.t4 | PANTHER | PTHR11722 | 60S RIBOSOMAL PROTEIN L13 | 2 | 208 | 6.0E-75 |
| 1 | g8374.t4 | Pfam | PF01294 | Ribosomal protein L13e | 6 | 188 | 2.2E-70 |
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.
