General information for g3358.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 28S ribosomal protein S5, mitochondrial.
Parent gene
- The parent gene g3358 is located on chr_3: 24831482..24832860 (- 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 | g3358 | g3358.t1 | TTS | g3358.t1 | 24830208 | 24830208 |
| chr_3 | g3358 | g3358.t1 | isoform | g3358.t1 | 24830260 | 24831721 |
| chr_3 | g3358 | g3358.t1 | exon | g3358.t1.exon1 | 24830260 | 24831138 |
| chr_3 | g3358 | g3358.t1 | cds | g3358.t1.CDS1 | 24830260 | 24831138 |
| chr_3 | g3358 | g3358.t1 | exon | g3358.t1.exon2 | 24831203 | 24831513 |
| chr_3 | g3358 | g3358.t1 | cds | g3358.t1.CDS2 | 24831203 | 24831513 |
| chr_3 | g3358 | g3358.t1 | exon | g3358.t1.exon3 | 24831577 | 24831721 |
| chr_3 | g3358 | g3358.t1 | cds | g3358.t1.CDS3 | 24831577 | 24831721 |
| chr_3 | g3358 | g3358.t1 | TSS | g3358.t1 | 24831795 | 24831795 |
Sequences
>g3358.t1 Gene=g3358 Length=1335
ATGGCACTTAAACTATTACAAAATGGAAGGCTTTTAACTCGAGCTTTTCAAAATTTACAT
ATAACACCAACAACATCAACTATTTTTGCTAAAAATAATGATTTGAATTTAAATTTTTCA
CGCAACACAAGTTTCTTCGTAAAATTGCCTGCAGAAGATTTATGGAAAGGAGTTACATCA
GTTTCAAATGCAGGAAGAAAAAGAGGTCGTGCGAAAGGTTTAGTAAGAAGAAAAGATTTG
AATCGTGGGCAAGTGATTGGTGTCGGTAAAGCAAATATTCAATGGCCTGGACTTTCGGCT
CCTATTATTCGTGGTAGAGAACTCATTCAAAGACAACAATTGCCACCAGATCCAGAACGA
GAAGCAAAATTGATTAAAATGCGTGATGCGATGAGTAGCAAAGGATATCAAAAATTGTCA
CCTCTTGATCGTGGTTGGACAGGTGCTAAATTAGGTGGACGAAGCATTGGAGCACCTGAT
CCAATTGGTGATGATAATTTTGAAGGCTTTGATACGAAAGTAATTGAATACAAGCAAGTT
TTTAATATGAAAGGTAATTTAGGAAGAAAACGAAGACTTTCTGCTTTTGTTGTAACTGGA
AATCATAATGGACTTGCCGGTTTTGCATCAGCTAAAGCAGTCGATGGAAAAGCTGTTTTG
AGAAAGGCTAAAAATCGCGCTGCACAAAAATTAATGTACATTGAATTATGTGATGGTCAT
ACAGTCTTTCATGACTTTTTTTGTCAATTTGGTTTAACTAAAATATTTGTCGAAAAAAAA
CCAGAAGGCTTCGGACTCGTATGTCATCGTGCTATTAGAGAAATTTGTCAACTTGTTGGT
ATCAAAAATCTTTATGCTAAAGTTGAAGGAGCAACTGGCGTTCAACATATTGTTAAAGCA
TTTTTCTTAGGATTATTAAAACAAAAGAAGTTTGAAGAAATTGCTGAATCAAAAGGACTT
CATCTTGTTGAATTTAAGCCTGAGCTTGGAAATTTCCCAAGAGTAGTTGCTAGTCCAAAA
GTATGTAGAAAAGAAGACGACATAAAATATGATGAAATTATGGACTATACACAAGTAGCA
ATGAATGGAAAAGTTGTATTAAAGAGAAAGAAATATCCACCATTTTATGCCAACACTTAT
GGCTATCACATTCATTTGAAGAAACTTGAAGGACGACGAAATCATTTCAAAATCAAATTC
GATATGCTTAAAGAACATGGAACAATCAAAAGTTTCCTCACTGACAAATATCCAGATGCA
CGACCACATGGTTTTATATTAAGAGATGCATACCTAAAAAAGAAAGCTGAAGGTGAAGAA
ACGAGTGCAGAATAA
>g3358.t1 Gene=g3358 Length=444
MALKLLQNGRLLTRAFQNLHITPTTSTIFAKNNDLNLNFSRNTSFFVKLPAEDLWKGVTS
VSNAGRKRGRAKGLVRRKDLNRGQVIGVGKANIQWPGLSAPIIRGRELIQRQQLPPDPER
EAKLIKMRDAMSSKGYQKLSPLDRGWTGAKLGGRSIGAPDPIGDDNFEGFDTKVIEYKQV
FNMKGNLGRKRRLSAFVVTGNHNGLAGFASAKAVDGKAVLRKAKNRAAQKLMYIELCDGH
TVFHDFFCQFGLTKIFVEKKPEGFGLVCHRAIREICQLVGIKNLYAKVEGATGVQHIVKA
FFLGLLKQKKFEEIAESKGLHLVEFKPELGNFPRVVASPKVCRKEDDIKYDEIMDYTQVA
MNGKVVLKRKKYPPFYANTYGYHIHLKKLEGRRNHFKIKFDMLKEHGTIKSFLTDKYPDA
RPHGFILRDAYLKKKAEGEETSAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3358.t1 | Gene3D | G3DSA:3.30.160.20 | - | 164 | 232 | 0.000 |
| 7 | g3358.t1 | Gene3D | G3DSA:3.30.230.10 | - | 236 | 326 | 0.000 |
| 3 | g3358.t1 | PANTHER | PTHR13718:SF90 | 28S RIBOSOMAL PROTEIN S5, MITOCHONDRIAL | 33 | 368 | 0.000 |
| 4 | g3358.t1 | PANTHER | PTHR13718 | RIBOSOMAL S SUBUNIT | 33 | 368 | 0.000 |
| 1 | g3358.t1 | Pfam | PF00333 | Ribosomal protein S5, N-terminal domain | 170 | 235 | 0.000 |
| 2 | g3358.t1 | Pfam | PF03719 | Ribosomal protein S5, C-terminal domain | 249 | 317 | 0.000 |
| 9 | g3358.t1 | ProSiteProfiles | PS50881 | S5 double stranded RNA-binding domain profile. | 170 | 234 | 10.877 |
| 6 | g3358.t1 | SUPERFAMILY | SSF54768 | dsRNA-binding domain-like | 166 | 236 | 0.000 |
| 5 | g3358.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 240 | 319 | 0.000 |
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:0003723 | RNA binding | MF |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02988 (small subunit ribosomal protein S5)
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.
