Gene loci information

Transcript annotation

  • This transcript has been annotated as 39S ribosomal protein L13, 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_2 g8647 g8647.t2 TTS g8647.t2 32081150 32081150
chr_2 g8647 g8647.t2 isoform g8647.t2 32081209 32081782
chr_2 g8647 g8647.t2 exon g8647.t2.exon1 32081209 32081606
chr_2 g8647 g8647.t2 cds g8647.t2.CDS1 32081209 32081606
chr_2 g8647 g8647.t2 exon g8647.t2.exon2 32081659 32081782
chr_2 g8647 g8647.t2 cds g8647.t2.CDS2 32081659 32081662
chr_2 g8647 g8647.t2 TSS g8647.t2 32081943 32081943

Sequences

>g8647.t2 Gene=g8647 Length=522
CAATGGGCAACTTTTGCTCGACAATGGCACATTTTTGATTGTAAATGGCAAAATCCATAT
GAAAGCGCAATTGCAATAGTTAAACATCTTAAAGGTCTTCATAAACCTATTTATCATCCT
ATGAATGATTGCGGAGATCATGTTATTTGTATAAATACGAAAGAAATTGCCCTTCCTGGC
AATGAGTGGACTAAAAGAGCATATTTTCATCATACTGGTTATCCAGGAGGTGCATCTTGG
ACTCTCGCTTGGGAATTGCATTCAAAAGATCCGGTGATGATTATGAAAAAGGCAATCTAC
AGACGTCTTGGAAATAATCTTCAACGCCGGTACACAATGCAAAGACTACACTTGTTTCCT
GATGATAATGTTCCTAAAGAATTGATAGAAAATGTCACAAGTCAAATAAGACAATTGAGA
GTAGTTCCGCAAAGAATAGATCACATTGAAAAGGATGTCATCGATAATTATCCAAAAATC
ATGGATTACCCTACTGATTACTTACCTAAAACATTAAAATAG

>g8647.t2 Gene=g8647 Length=133
MNDCGDHVICINTKEIALPGNEWTKRAYFHHTGYPGGASWTLAWELHSKDPVMIMKKAIY
RRLGNNLQRRYTMQRLHLFPDDNVPKELIENVTSQIRQLRVVPQRIDHIEKDVIDNYPKI
MDYPTDYLPKTLK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g8647.t2 CDD cd00392 Ribosomal_L13 3 82 0
5 g8647.t2 Gene3D G3DSA:3.90.1180.10 - 1 128 0
2 g8647.t2 PANTHER PTHR11545:SF2 39S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL 2 111 0
3 g8647.t2 PANTHER PTHR11545 RIBOSOMAL PROTEIN L13 2 111 0
6 g8647.t2 PIRSF PIRSF002181 RPL13p_RPL13Aa_RPL16e_RPL13o 1 128 0
1 g8647.t2 Pfam PF00572 Ribosomal protein L13 2 85 0
4 g8647.t2 SUPERFAMILY SSF52161 Ribosomal protein L13 2 97 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.

Raw TPM values