General information for g13545.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13545 is located on chr_1: 30802285..30803644 (- 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 | g13545 | g13545.t4 | TTS | g13545.t4 | 30802222 | 30802222 |
| chr_1 | g13545 | g13545.t4 | isoform | g13545.t4 | 30802285 | 30803108 |
| chr_1 | g13545 | g13545.t4 | exon | g13545.t4.exon1 | 30802285 | 30802608 |
| chr_1 | g13545 | g13545.t4 | cds | g13545.t4.CDS1 | 30802285 | 30802608 |
| chr_1 | g13545 | g13545.t4 | exon | g13545.t4.exon2 | 30802727 | 30803108 |
| chr_1 | g13545 | g13545.t4 | cds | g13545.t4.CDS2 | 30802727 | 30802729 |
| chr_1 | g13545 | g13545.t4 | TSS | g13545.t4 | 30803370 | 30803370 |
Sequences
>g13545.t4 Gene=g13545 Length=706
ATGCAATTACACATTCGTGGTCAGCAAAACCATGTGTTGGAAGTCCAACCAGAGGAAACT
GTTTCAATTATTAAGGTAAGTTTTTTGTTGCAAAAGAAAGAATCAACTAGAAAATATTCT
GCAGTTACTCAGCTGGTCATGAAACTCAAGTTTTTACTGTATTCCTGACCTTCCTAATTA
CTGCTAAATCAAATCATTGTTCATCTATTTGAAGATATTGTGTTGAAAAAGTACCAAATG
TCTCGAGCGGTGTTCAAACAGTGAAATTTGTTGTTATTTAAAATTATGGAAATTATCGCA
GATCTACCGAATCTCTTGTTCTGTATATTAATAAGCTTGAGATACCAAACCTTTCTGCAA
TAGCATCTTGTTATGATCCATGGCTAAATTAGCAGTTCTTGAAAATGTTGACATCAATAC
TGAAATGACACTTGCTTGTGAAGGCATTATTCTCGCTGATAACGATACAGTTTCAGAACT
CAGCAATGTTGAATTAGACCTTACAATCCCACTTCTTGGTGGTAAAGTTCACGGTTCTTT
GGCACGTGCTGGAAAAGTTAAAGGACAAACACCAAAAGTAGAGAAACAGGAAAAGAGAAA
GAAGAAGACAGGACGTGCTAAGAGACGCATTCAATTCAACCGCCGTTTTGCTAATGTTGT
CCAAGGCTTTGGTCGCAAACGTGGACCTAACGCTAATTCCTCATAA
>g13545.t4 Gene=g13545 Length=108
MAKLAVLENVDINTEMTLACEGIILADNDTVSELSNVELDLTIPLLGGKVHGSLARAGKV
KGQTPKVEKQEKRKKKTGRAKRRIQFNRRFANVVQGFGRKRGPNANSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g13545.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 57 | 82 | - |
| 2 | g13545.t4 | PANTHER | PTHR12650 | 40S RIBOSOMAL PROTEIN S30/UBIQUITIN-LIKE PROTEIN FUBI | 36 | 107 | 4.8E-36 |
| 3 | g13545.t4 | PANTHER | PTHR12650:SF15 | 40S RIBOSOMAL PROTEIN S30 | 36 | 107 | 4.8E-36 |
| 1 | g13545.t4 | Pfam | PF04758 | Ribosomal protein S30 | 49 | 106 | 9.9E-29 |
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 K02983 (small subunit ribosomal protein S30e)
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. There were no conditions that were differentially expressed