General information for g13545.t1
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.t1 | TTS | g13545.t1 | 30802222 | 30802222 |
| chr_1 | g13545 | g13545.t1 | isoform | g13545.t1 | 30802285 | 30803108 |
| chr_1 | g13545 | g13545.t1 | exon | g13545.t1.exon1 | 30802285 | 30802608 |
| chr_1 | g13545 | g13545.t1 | cds | g13545.t1.CDS1 | 30802285 | 30802608 |
| chr_1 | g13545 | g13545.t1 | exon | g13545.t1.exon2 | 30803034 | 30803108 |
| chr_1 | g13545 | g13545.t1 | cds | g13545.t1.CDS2 | 30803034 | 30803108 |
| chr_1 | g13545 | g13545.t1 | TSS | g13545.t1 | 30803370 | 30803370 |
Sequences
>g13545.t1 Gene=g13545 Length=399
ATGCAATTACACATTCGTGGTCAGCAAAACCATGTGTTGGAAGTCCAACCAGAGGAAACT
GTTTCAATTATTAAGGCTAAATTAGCAGTTCTTGAAAATGTTGACATCAATACTGAAATG
ACACTTGCTTGTGAAGGCATTATTCTCGCTGATAACGATACAGTTTCAGAACTCAGCAAT
GTTGAATTAGACCTTACAATCCCACTTCTTGGTGGTAAAGTTCACGGTTCTTTGGCACGT
GCTGGAAAAGTTAAAGGACAAACACCAAAAGTAGAGAAACAGGAAAAGAGAAAGAAGAAG
ACAGGACGTGCTAAGAGACGCATTCAATTCAACCGCCGTTTTGCTAATGTTGTCCAAGGC
TTTGGTCGCAAACGTGGACCTAACGCTAATTCCTCATAA
>g13545.t1 Gene=g13545 Length=132
MQLHIRGQQNHVLEVQPEETVSIIKAKLAVLENVDINTEMTLACEGIILADNDTVSELSN
VELDLTIPLLGGKVHGSLARAGKVKGQTPKVEKQEKRKKKTGRAKRRIQFNRRFANVVQG
FGRKRGPNANSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13545.t1 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 104 | 2.1E-6 |
| 7 | g13545.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 81 | 106 | - |
| 3 | g13545.t1 | PANTHER | PTHR12650:SF30 | 40S RIBOSOMAL PROTEIN S30 | 2 | 131 | 1.1E-42 |
| 4 | g13545.t1 | PANTHER | PTHR12650 | 40S RIBOSOMAL PROTEIN S30/UBIQUITIN-LIKE PROTEIN FUBI | 2 | 131 | 1.1E-42 |
| 2 | g13545.t1 | Pfam | PF00240 | Ubiquitin family | 8 | 69 | 5.1E-7 |
| 1 | g13545.t1 | Pfam | PF04758 | Ribosomal protein S30 | 73 | 130 | 1.6E-28 |
| 9 | g13545.t1 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 1 | 59 | 10.419 |
| 6 | g13545.t1 | SMART | SM00213 | ubq_7 | 1 | 72 | 8.7E-6 |
| 5 | g13545.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 3 | 94 | 5.89E-9 |
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:0005515 | protein binding | MF |
| 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.
