Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t6 TTS g3358.t6 24830208 24830208
chr_3 g3358 g3358.t6 isoform g3358.t6 24830564 24831721
chr_3 g3358 g3358.t6 exon g3358.t6.exon1 24830564 24831138
chr_3 g3358 g3358.t6 cds g3358.t6.CDS1 24830566 24831138
chr_3 g3358 g3358.t6 exon g3358.t6.exon2 24831203 24831513
chr_3 g3358 g3358.t6 cds g3358.t6.CDS2 24831203 24831513
chr_3 g3358 g3358.t6 exon g3358.t6.exon3 24831573 24831721
chr_3 g3358 g3358.t6 cds g3358.t6.CDS3 24831573 24831573
chr_3 g3358 g3358.t6 TSS g3358.t6 24831795 24831795

Sequences

>g3358.t6 Gene=g3358 Length=1035
ATGGCACTTAAACTATTACAAAATGGAAGGCTTTTAACTCGAGCTTTTCAAAATTTACAT
ATAACACCAACAACATCAACTATTTTTGCTAAAAATAATGATTTGAATTTAAATTTTTCA
CGCAACACAAGTTTCTTCGTAAAATGTGATGCCTGCAGAAGATTTATGGAAAGGAGTTAC
ATCAGTTTCAAATGCAGGAAGAAAAAGAGGTCGTGCGAAAGGTTTAGTAAGAAGAAAAGA
TTTGAATCGTGGGCAAGTGATTGGTGTCGGTAAAGCAAATATTCAATGGCCTGGACTTTC
GGCTCCTATTATTCGTGGTAGAGAACTCATTCAAAGACAACAATTGCCACCAGATCCAGA
ACGAGAAGCAAAATTGATTAAAATGCGTGATGCGATGAGTAGCAAAGGATATCAAAAATT
GTCACCTCTTGATCGTGGTTGGACAGGTGCTAAATTAGGTGGACGAAGCATTGGAGCACC
TGATCCAATTGGTGATGATAATTTTGAAGGCTTTGATACGAAAGTAATTGAATACAAGCA
AGTTTTTAATATGAAAGGTAATTTAGGAAGAAAACGAAGACTTTCTGCTTTTGTTGTAAC
TGGAAATCATAATGGACTTGCCGGTTTTGCATCAGCTAAAGCAGTCGATGGAAAAGCTGT
TTTGAGAAAGGCTAAAAATCGCGCTGCACAAAAATTAATGTACATTGAATTATGTGATGG
TCATACAGTCTTTCATGACTTTTTTTGTCAATTTGGTTTAACTAAAATATTTGTCGAAAA
AAAACCAGAAGGCTTCGGACTCGTATGTCATCGTGCTATTAGAGAAATTTGTCAACTTGT
TGGTATCAAAAATCTTTATGCTAAAGTTGAAGGAGCAACTGGCGTTCAACATATTGTTAA
AGCATTTTTCTTAGGATTATTAAAACAAAAGAAGTTTGAAGAAATTGCTGAATCAAAAGG
ACTTCATCTTGTTGAATTTAAGCCTGAGCTTGGAAATTTCCCAAGAGTAGTTGCTAGTCC
AAAAGTATGTAGAAA

>g3358.t6 Gene=g3358 Length=295
MPAEDLWKGVTSVSNAGRKRGRAKGLVRRKDLNRGQVIGVGKANIQWPGLSAPIIRGREL
IQRQQLPPDPEREAKLIKMRDAMSSKGYQKLSPLDRGWTGAKLGGRSIGAPDPIGDDNFE
GFDTKVIEYKQVFNMKGNLGRKRRLSAFVVTGNHNGLAGFASAKAVDGKAVLRKAKNRAA
QKLMYIELCDGHTVFHDFFCQFGLTKIFVEKKPEGFGLVCHRAIREICQLVGIKNLYAKV
EGATGVQHIVKAFFLGLLKQKKFEEIAESKGLHLVEFKPELGNFPRVVASPKVCR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3358.t6 Gene3D G3DSA:3.30.160.20 - 116 184 0.000
7 g3358.t6 Gene3D G3DSA:3.30.230.10 - 188 278 0.000
3 g3358.t6 PANTHER PTHR13718:SF90 28S RIBOSOMAL PROTEIN S5, MITOCHONDRIAL 3 292 0.000
4 g3358.t6 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 3 292 0.000
1 g3358.t6 Pfam PF00333 Ribosomal protein S5, N-terminal domain 122 187 0.000
2 g3358.t6 Pfam PF03719 Ribosomal protein S5, C-terminal domain 201 269 0.000
9 g3358.t6 ProSiteProfiles PS50881 S5 double stranded RNA-binding domain profile. 122 186 10.877
6 g3358.t6 SUPERFAMILY SSF54768 dsRNA-binding domain-like 118 188 0.000
5 g3358.t6 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 192 271 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

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. There were no conditions that were differentially expressed