Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 28S ribosomal protein S5, mitochondrial.

Parent gene

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.t4 TTS g3358.t4 24830208 24830208
chr_3 g3358 g3358.t4 isoform g3358.t4 24830260 24831721
chr_3 g3358 g3358.t4 exon g3358.t4.exon1 24830260 24831138
chr_3 g3358 g3358.t4 cds g3358.t4.CDS1 24830260 24831138
chr_3 g3358 g3358.t4 exon g3358.t4.exon2 24831203 24831721
chr_3 g3358 g3358.t4 cds g3358.t4.CDS2 24831203 24831280
chr_3 g3358 g3358.t4 TSS g3358.t4 24831795 24831795

Sequences

>g3358.t4 Gene=g3358 Length=1398
ATGGCACTTAAACTATTACAAAATGGAAGGCTTTTAACTCGAGCTTTTCAAAATTTACAT
ATAACACCAACAACATCAACTATTTTTGCTAAAAATAATGATTTGAATTTAAATTTTTCA
CGCAACACAAGTTTCTTCGTAAAATGTGAGTGAAAATTATTGCAAATTTAAAATTCCCAT
ATTATTTATTATTCTGTTCTAATTTTAGTGCCTGCAGAAGATTTATGGAAAGGAGTTACA
TCAGTTTCAAATGCAGGAAGAAAAAGAGGTCGTGCGAAAGGTTTAGTAAGAAGAAAAGAT
TTGAATCGTGGGCAAGTGATTGGTGTCGGTAAAGCAAATATTCAATGGCCTGGACTTTCG
GCTCCTATTATTCGTGGTAGAGAACTCATTCAAAGACAACAATTGCCACCAGATCCAGAA
CGAGAAGCAAAATTGATTAAAATGCGTGATGCGATGAGTAGCAAAGGATATCAAAAATTG
TCACCTCTTGATCGTGGTTGGACAGGTGCTAAATTAGGTGGACGAAGCATTGGAGCACCT
GATCCAATTGGTGATGATAATTTTGAAGGCTTTGATACGAAAGTAATTGAATACAAGCAA
GTTTTTAATATGAAAGGTAATTTAGGAAGAAAACGAAGACTTTCTGCTTTTGTTGTAACT
GGAAATCATAATGGACTTGCCGGTTTTGCATCAGCTAAAGCAGTCGATGGAAAAGCTGTT
TTGAGAAAGGCTAAAAATCGCGCTGCACAAAAATTAATGTACATTGAATTATGTGATGGT
CATACAGTCTTTCATGACTTTTTTTGTCAATTTGGTTTAACTAAAATATTTGTCGAAAAA
AAACCAGAAGGCTTCGGACTCGTATGTCATCGTGCTATTAGAGAAATTTGTCAACTTGTT
GGTATCAAAAATCTTTATGCTAAAGTTGAAGGAGCAACTGGCGTTCAACATATTGTTAAA
GCATTTTTCTTAGGATTATTAAAACAAAAGAAGTTTGAAGAAATTGCTGAATCAAAAGGA
CTTCATCTTGTTGAATTTAAGCCTGAGCTTGGAAATTTCCCAAGAGTAGTTGCTAGTCCA
AAAGTATGTAGAAAAGAAGACGACATAAAATATGATGAAATTATGGACTATACACAAGTA
GCAATGAATGGAAAAGTTGTATTAAAGAGAAAGAAATATCCACCATTTTATGCCAACACT
TATGGCTATCACATTCATTTGAAGAAACTTGAAGGACGACGAAATCATTTCAAAATCAAA
TTCGATATGCTTAAAGAACATGGAACAATCAAAAGTTTCCTCACTGACAAATATCCAGAT
GCACGACCACATGGTTTTATATTAAGAGATGCATACCTAAAAAAGAAAGCTGAAGGTGAA
GAAACGAGTGCAGAATAA

>g3358.t4 Gene=g3358 Length=318
MRDAMSSKGYQKLSPLDRGWTGAKLGGRSIGAPDPIGDDNFEGFDTKVIEYKQVFNMKGN
LGRKRRLSAFVVTGNHNGLAGFASAKAVDGKAVLRKAKNRAAQKLMYIELCDGHTVFHDF
FCQFGLTKIFVEKKPEGFGLVCHRAIREICQLVGIKNLYAKVEGATGVQHIVKAFFLGLL
KQKKFEEIAESKGLHLVEFKPELGNFPRVVASPKVCRKEDDIKYDEIMDYTQVAMNGKVV
LKRKKYPPFYANTYGYHIHLKKLEGRRNHFKIKFDMLKEHGTIKSFLTDKYPDARPHGFI
LRDAYLKKKAEGEETSAE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3358.t4 Gene3D G3DSA:3.30.160.20 - 38 106 0.000
7 g3358.t4 Gene3D G3DSA:3.30.230.10 - 110 200 0.000
3 g3358.t4 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 2 216 0.000
4 g3358.t4 PANTHER PTHR13718:SF61 28S RIBOSOMAL PROTEIN S5, MITOCHONDRIAL 2 216 0.000
1 g3358.t4 Pfam PF00333 Ribosomal protein S5, N-terminal domain 44 109 0.000
2 g3358.t4 Pfam PF03719 Ribosomal protein S5, C-terminal domain 123 191 0.000
9 g3358.t4 ProSiteProfiles PS50881 S5 double stranded RNA-binding domain profile. 44 108 10.877
6 g3358.t4 SUPERFAMILY SSF54768 dsRNA-binding domain-like 40 110 0.000
5 g3358.t4 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 114 193 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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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.

Raw TPM values