General information for g4897.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 28S ribosomal protein S10, mitochondrial.
Parent gene
- The parent gene g4897 is located on chr_2: 5845597..5846105 (+ 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 | g4897 | g4897.t7 | TSS | g4897.t7 | 5845459 | 5845459 |
| chr_2 | g4897 | g4897.t7 | isoform | g4897.t7 | 5845517 | 5846105 |
| chr_2 | g4897 | g4897.t7 | exon | g4897.t7.exon1 | 5845517 | 5845531 |
| chr_2 | g4897 | g4897.t7 | cds | g4897.t7.CDS1 | 5845517 | 5845531 |
| chr_2 | g4897 | g4897.t7 | exon | g4897.t7.exon2 | 5845602 | 5846105 |
| chr_2 | g4897 | g4897.t7 | cds | g4897.t7.CDS2 | 5845602 | 5846105 |
| chr_2 | g4897 | g4897.t7 | TTS | g4897.t7 | 5846135 | 5846135 |
Sequences
>g4897.t7 Gene=g4897 Length=519
ATGAATATTTTGCAGATCAATAGCATTATACCAGCGTCTTCAAAGCGCATATTTTCACAA
AATTATTTAAGATTGTTTTCGTCAACAATAACGCAACCTCAAACCATTGGTGAAAATGAA
ATTGCTGTTCCTCAAAAAGACAAACTGTATTCTCGATTAGAAATTGAGTTGAAAGGTATT
GAGCCAGAAGTGATGAGAAGTTATGCATGGTATGCACAAAAATCAGCAGAACATTTAGGT
ATTAAAATTGGAAGATGTTATGCAGCAAGAAAATCAGAAAAGGATCGTTGGACAGTGCTT
AAAAGTGTTCATGTTCATGCAAAGCATTTAGTTTCATATGAAGCACGAACTTATTATCGC
TTTATGAATTTTCACAACCTCACACAATCAACTCTCGAGACTTTTCTTGAATATATTCAA
AGAAATTTGCCAGAGGGTACAGCAATGAAAGCAACTAAAATTGAAATTCAACCTTTACCA
GAACATATAGTTAAGTCTATTGAAGAAAATGCAAAATAA
>g4897.t7 Gene=g4897 Length=172
MNILQINSIIPASSKRIFSQNYLRLFSSTITQPQTIGENEIAVPQKDKLYSRLEIELKGI
EPEVMRSYAWYAQKSAEHLGIKIGRCYAARKSEKDRWTVLKSVHVHAKHLVSYEARTYYR
FMNFHNLTQSTLETFLEYIQRNLPEGTAMKATKIEIQPLPEHIVKSIEENAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4897.t7 | Gene3D | G3DSA:3.30.70.600 | - | 42 | 172 | 0 |
| 2 | g4897.t7 | PANTHER | PTHR13334 | MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S10 | 29 | 170 | 0 |
| 1 | g4897.t7 | Pfam | PF00338 | Ribosomal protein S10p/S20e | 54 | 151 | 0 |
| 4 | g4897.t7 | SMART | SM01403 | Ribosomal_S10_2 | 54 | 152 | 0 |
| 3 | g4897.t7 | SUPERFAMILY | SSF54999 | Ribosomal protein S10 | 53 | 151 | 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:0005763 | mitochondrial small ribosomal subunit | CC |
KEGG
Orthology
- This transcript has been annotated with K02946 (small subunit ribosomal protein S10)
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.
