Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 39S ribosomal protein L3, 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 g720 g720.t5 TSS g720.t5 5501415 5501415
chr_3 g720 g720.t5 isoform g720.t5 5501500 5502692
chr_3 g720 g720.t5 exon g720.t5.exon1 5501500 5502219
chr_3 g720 g720.t5 cds g720.t5.CDS1 5502194 5502219
chr_3 g720 g720.t5 exon g720.t5.exon2 5502272 5502692
chr_3 g720 g720.t5 cds g720.t5.CDS2 5502272 5502692
chr_3 g720 g720.t5 TTS g720.t5 5502747 5502747

Sequences

>g720.t5 Gene=g720 Length=1141
ATGTTTTTATCAAAAACCATAAAAACTGTTTTAGGTACTTCAATTATTAATGATGTTAGG
TAAATATCAAGCAGGAAAATGTTTAAAATGAGAAAAATAATAATTTTCTTTAACCTTTTT
TAAAGATACACACAAGTTTGTTTCCATCGATTTAAATTTATCCCTAAATTACGAGTACCT
GAATGGCATTTTAGAGTCGAAAGAAGAGCAAAGGACCGAGATGATAATCTGACGGAAAGA
AATAAAAGATTTATCAATGAAATGTCGAAAAAAGATCATGAAAAAGCATCTTTATTAAAA
GTACCGACAGTTGAACCAAAAGAATGGAAGAAAGGAATGATTCGTTGTGGAATAGTTGCT
AAAAAGCTAGGCTATTATCCTCTTTGGACAAAAGATGGTACTCGAATTTGTACGACAGTT
TTACAAATCATTGAAAATCATGTCATTAAATATGCACCACCTGGAGAATTCAATCCTACA
ATGAGAAAACGTCTAGGTAATTACAATAAAAAAGGTTGTCTCTATATAGGATCAGGAGAA
GCTGATCCAAACCGATTGACAGCAAATTACATGGGTTTATTTAAAGAAAGTGGTGTGATG
CCAACACAAAGAATTACGCGTTTTATCATACATCCTGATGCAGCACTTCCTATAGGCACA
TCAATCAATGCTCTTCATTATCGTGTTGGTGATTATGTTGATGTATTGGGTAAAACGTAA
CGTTGATCAAGGCTGGCAAGGTGTCATTAAAAGATGGGGATTTAAAGGAGGACCAGCAAC
TCATGGAACTACTAAAAATCATAGACGTGGAGGATCTTTGGCTTCAGGCATTAAAAGTAG
AATTTGGAAAGGAAAGAAAATGCCTGGAAATATGGGGAATCGATGGAGAACTCTTCGTGG
TTTAAAAATTTGGAGAATTAATAGAAAAGAAAATTGTATTTGGGTGTCAGGTAGAGCAAT
CGCAGGAGCACCTGGAAGTTTAGTTTATATTTATGATACAGTTTTACCACTTCGTCAACC
TAAAGAACCTCTTCATTTTCCAACTTTTCTCGGTGATGAGTCAAAATTACCTGAAGACAT
TTATGAAGAAACAATTCACAAATTTGGAGATTTGACGATAACATTTGAGCCCGAGAAATA
A

>g720.t5 Gene=g720 Length=148
MLMYWVKRNVDQGWQGVIKRWGFKGGPATHGTTKNHRRGGSLASGIKSRIWKGKKMPGNM
GNRWRTLRGLKIWRINRKENCIWVSGRAIAGAPGSLVYIYDTVLPLRQPKEPLHFPTFLG
DESKLPEDIYEETIHKFGDLTITFEPEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g720.t5 Gene3D G3DSA:2.40.30.10 Translation factors 15 105 0
2 g720.t5 PANTHER PTHR11229 50S RIBOSOMAL PROTEIN L3 9 141 0
1 g720.t5 Pfam PF00297 Ribosomal protein L3 12 79 0
3 g720.t5 SUPERFAMILY SSF50447 Translation proteins 12 124 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:0005840 ribosome CC
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. There were no conditions that were differentially expressed