General information for g4089.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 28S ribosomal protein S14, mitochondrial.
Parent gene
- The parent gene g4089 is located on chr_3: 30513763..30514229 (+ 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_3 | g4089 | g4089.t1 | TSS | g4089.t1 | 30513737 | 30513737 |
| chr_3 | g4089 | g4089.t1 | isoform | g4089.t1 | 30513763 | 30514229 |
| chr_3 | g4089 | g4089.t1 | exon | g4089.t1.exon1 | 30513763 | 30513834 |
| chr_3 | g4089 | g4089.t1 | cds | g4089.t1.CDS1 | 30513763 | 30513834 |
| chr_3 | g4089 | g4089.t1 | exon | g4089.t1.exon2 | 30513897 | 30514229 |
| chr_3 | g4089 | g4089.t1 | cds | g4089.t1.CDS2 | 30513897 | 30514229 |
| chr_3 | g4089 | g4089.t1 | TTS | g4089.t1 | 30514294 | 30514294 |
Sequences
>g4089.t1 Gene=g4089 Length=405
ATGTCTTTTATTTCAAGTCTATCATCAACAGCAAACAGTTTAATTCGATCAAGTGCATCA
AAATTATTTGGATTCACTCAAAAGAGATCAGGAGCAGGATGGACAGACTGGAGAATGATT
AAAGATAACAAAAGACGGTTGCTTGTAAAAGAGCATGCTGTGGATCGTTTAAGATTAAAT
ACTCTTCGAAAAAATAATATCCTTCCTGTAGAACTACGAGAAATTGCAAGTCAAGAGCTT
CACAATAATTTTCCCAGAGATGCATGCTTAAATCGAGTCGTATATAGATGCATGCTAACA
AGTAGACCAAGAGGAACAGTAATTAAATTTAGAACTAGTCGTATAATGTTCCGACATTTG
GCTGATTATAATAAGCTATCTGGAATTCAGAGAGCTATGTGGTAA
>g4089.t1 Gene=g4089 Length=134
MSFISSLSSTANSLIRSSASKLFGFTQKRSGAGWTDWRMIKDNKRRLLVKEHAVDRLRLN
TLRKNNILPVELREIASQELHNNFPRDACLNRVVYRCMLTSRPRGTVIKFRTSRIMFRHL
ADYNKLSGIQRAMW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4089.t1 | Gene3D | G3DSA:4.10.830.10 | 30s Ribosomal Protein S14; Chain N | 76 | 134 | 0 |
| 2 | g4089.t1 | PANTHER | PTHR19836 | 30S RIBOSOMAL PROTEIN S14 | 32 | 134 | 0 |
| 3 | g4089.t1 | PANTHER | PTHR19836:SF19 | 28S RIBOSOMAL PROTEIN S14, MITOCHONDRIAL | 32 | 134 | 0 |
| 1 | g4089.t1 | Pfam | PF00253 | Ribosomal protein S14p/S29e | 82 | 132 | 0 |
| 4 | g4089.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 35 | 134 | 0 |
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 K02954 (small subunit ribosomal protein S14)
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.
