General information for g8374.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t28 | TTS | g8374.t28 | 30066432 | 30066432 |
| chr_2 | g8374 | g8374.t28 | isoform | g8374.t28 | 30066515 | 30067691 |
| chr_2 | g8374 | g8374.t28 | exon | g8374.t28.exon1 | 30066515 | 30066933 |
| chr_2 | g8374 | g8374.t28 | cds | g8374.t28.CDS1 | 30066826 | 30066933 |
| chr_2 | g8374 | g8374.t28 | exon | g8374.t28.exon2 | 30066992 | 30067245 |
| chr_2 | g8374 | g8374.t28 | cds | g8374.t28.CDS2 | 30066992 | 30067228 |
| chr_2 | g8374 | g8374.t28 | exon | g8374.t28.exon3 | 30067659 | 30067691 |
| chr_2 | g8374 | g8374.t28 | TSS | g8374.t28 | 30067694 | 30067694 |
Sequences
>g8374.t28 Gene=g8374 Length=706
TTTCTCATAATTTTCTTGTCCAACGAGTTGAAAATTAACCCTAACTCAAAATGAAGGGCA
ATCAAATGATTCCAAATGCCCACTTTCACAAGTGGTGGCAACGATTTGTGAGAACTTGGT
TCAATCAACCAGCCAGAAAATATCGTCGTCGTCAGAATCGTATTGCAAAAGCTAAAGCAG
CTTTCCCAAGACCTGCATCAAAATTGCGACCAATTGTAAGATGTCCATCAATCCGTTATT
CAACAAAACTCAGAATGGGACGTGGATTTTCATTGGCTGAATTGAAGAGGCTGCTGGTCT
CACAGCTGGTTTTGCCCGATCTGTGGGTATTTCAGTTGATCGTCGTCGTCGCAACAAGTC
GGTTGAATCAAGACAACAGAATGTTCAACGCTTGAAGGAATATCAAAATAAACTCATCCT
CTTCCCAGTTCATGAAAATAAGAAGAACTTGAAATTGCGAAAGGGTGAAGCAACAGAAGA
AGAACGTAAATTGGCTACACAATTGACAGGTCCTATAATGCCACTCGTTAAACCTAAACC
AACCATTGAATTCCGCGCAATTAAGGAAGATGAAAAGAAGTTCTCTGCCTTCAATGCTAT
CCACTGCGCTCGTGTTGCTGCTCGTACAGCTGGCAAACGCGCAAAGGCTGCTAAAGATGC
TGCAGATGCCGCAGAAAATGCACCAGGAGCCAAGAAGGATAAATAA
>g8374.t28 Gene=g8374 Length=114
MKGNQMIPNAHFHKWWQRFVRTWFNQPARKYRRRQNRIAKAKAAFPRPASKLRPIVRCPS
IRYSTKLRMGRGFSLAELKRLLVSQLVLPDLWVFQLIVVVATSRLNQDNRMFNA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g8374.t28 | PANTHER | PTHR11722:SF0 | 60S RIBOSOMAL PROTEIN L13 | 2 | 79 | 1.2E-32 |
| 3 | g8374.t28 | PANTHER | PTHR11722 | 60S RIBOSOMAL PROTEIN L13 | 2 | 79 | 1.2E-32 |
| 1 | g8374.t28 | Pfam | PF01294 | Ribosomal protein L13e | 6 | 81 | 4.3E-37 |
| 4 | g8374.t28 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 80 | - |
| 6 | g8374.t28 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 101 | - |
| 5 | g8374.t28 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 102 | 114 | - |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
