General information for g7475.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 28S ribosomal protein S18b, mitochondrial.
Parent gene
- The parent gene g7475 is located on chr_2: 23915935..23916603 (+ 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 | g7475 | g7475.t1 | TSS | g7475.t1 | 23915915 | 23915915 |
| chr_2 | g7475 | g7475.t1 | isoform | g7475.t1 | 23915935 | 23916603 |
| chr_2 | g7475 | g7475.t1 | exon | g7475.t1.exon1 | 23915935 | 23916384 |
| chr_2 | g7475 | g7475.t1 | cds | g7475.t1.CDS1 | 23915935 | 23916384 |
| chr_2 | g7475 | g7475.t1 | exon | g7475.t1.exon2 | 23916448 | 23916603 |
| chr_2 | g7475 | g7475.t1 | cds | g7475.t1.CDS2 | 23916448 | 23916603 |
| chr_2 | g7475 | g7475.t1 | TTS | g7475.t1 | 23916663 | 23916663 |
Sequences
>g7475.t1 Gene=g7475 Length=606
ATGATGAATTTTCTTACAAAAATAGCGTGTTCTTCAAATTTATTCAAATTAAATAATTTA
TCGCCATATTCGAGTGCATTAGTGAAAAGTATAGTAACAACTAATGTTTATTATTGTGAA
GCACATGAGAATCAAGAAGCTGAAAAGGAGCAAATAAAAGAAAAGATTGATCCATCAATC
GATAGAACAAAAATAATTCCGGTTGAGACATCAATTCGATATTTAAAGAGTGCTGCATAT
AAAGAAACATATGGTGATCAAGCAGTTTGGATTCCTTATCGACGAAATCATAAAGGCTTA
ATTCCTCCCAGAAAAACAAGAAAAACTTGCATTCGAAAAGGAAAAATTGCCACTGGAAGT
CCTTGTCCAATCTGTCGTGACGAATATCTTGTGCTTCATCACGAAAATACAGATCTTTTA
AAACAATTTATATCACCTCAAACAGGACAAGTGCTTAGTTTCTCAAAAACAGGATTGTGT
CAGAAGAAGCATTTACAATTGCTACTTGCAGTTGAAAGAGCAAAAGACCACGGTCGAATT
GTGTACGACGTTCCACAGAGAGACTATTCAGAATATTATGAGCAATATGCAAACAAGTCT
TCATAG
>g7475.t1 Gene=g7475 Length=201
MMNFLTKIACSSNLFKLNNLSPYSSALVKSIVTTNVYYCEAHENQEAEKEQIKEKIDPSI
DRTKIIPVETSIRYLKSAAYKETYGDQAVWIPYRRNHKGLIPPRKTRKTCIRKGKIATGS
PCPICRDEYLVLHHENTDLLKQFISPQTGQVLSFSKTGLCQKKHLQLLLAVERAKDHGRI
VYDVPQRDYSEYYEQYANKSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g7475.t1 | Gene3D | G3DSA:4.10.640.10 | 30s Ribosomal Protein S18 | 100 | 184 | 5e-07 |
| 2 | g7475.t1 | PANTHER | PTHR13329 | MITOCHONDRIAL RIBOSOMAL PROTEIN S18B | 23 | 196 | 0e+00 |
| 1 | g7475.t1 | Pfam | PF01084 | Ribosomal protein S18 | 132 | 178 | 0e+00 |
| 3 | g7475.t1 | SUPERFAMILY | SSF46911 | Ribosomal protein S18 | 113 | 186 | 0e+00 |
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:0032543 | mitochondrial translation | BP |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K16174 (small subunit ribosomal protein S18b, mitochondrial)
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.
