Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S12, 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_1 g10171 g10171.t2 TSS g10171.t2 8043820 8043820
chr_1 g10171 g10171.t2 isoform g10171.t2 8043837 8045460
chr_1 g10171 g10171.t2 exon g10171.t2.exon1 8043837 8043927
chr_1 g10171 g10171.t2 exon g10171.t2.exon2 8043992 8044067
chr_1 g10171 g10171.t2 cds g10171.t2.CDS1 8044016 8044067
chr_1 g10171 g10171.t2 exon g10171.t2.exon3 8045047 8045253
chr_1 g10171 g10171.t2 cds g10171.t2.CDS2 8045047 8045253
chr_1 g10171 g10171.t2 exon g10171.t2.exon4 8045309 8045460
chr_1 g10171 g10171.t2 cds g10171.t2.CDS3 8045309 8045460
chr_1 g10171 g10171.t2 TTS g10171.t2 8045497 8045497

Sequences

>g10171.t2 Gene=g10171 Length=526
AAAAAATTCTTGAAAATTTTATTTTACACAATTTTCTAGTAGATTTAGACATTAATTCAG
GCTAAAACATTAACATTTGGAAAGTTCAAAGCATTAAAACATTTTGTCGGAAAAAATGAA
TTTTTTAAAGCAAATGTTTAATGTTGCAAAGTTGCTCACAACTGAAGCTATTACAACTAT
TCAAACTTGTAATGGATCATCTTTAAATCAAATGCATCGAAAAGGACCTCATTATAAATT
TCGCCCACTTAGACAACCGTTAGATGGAAAACCGTTTGCTAAAGGTGTTGTGCTTAAAAC
ACTCATCAAAAAACCCAAAAAACCAAACTCTGCAAATCGTAAATGTGTACTTGTAAGACT
ATCAACGGGAAAAGAAATGGTCGCATATATTCCTGGAATTGGTCACAATCTACAAGAGCA
TAATGTTGTACTATGTCGTGTTGGTAGACTTCGTGATACTCCTGGTGTAAAAATTAAATG
TGTACGAGGAGCATACGATTTAGCTCATGTTATAAAAAAACAATAA

>g10171.t2 Gene=g10171 Length=136
MNFLKQMFNVAKLLTTEAITTIQTCNGSSLNQMHRKGPHYKFRPLRQPLDGKPFAKGVVL
KTLIKKPKKPNSANRKCVLVRLSTGKEMVAYIPGIGHNLQEHNVVLCRVGRLRDTPGVKI
KCVRGAYDLAHVIKKQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10171.t2 CDD cd03368 Ribosomal_S12 29 135 6.83368E-54
10 g10171.t2 Gene3D G3DSA:2.40.50.140 - 28 136 4.4E-46
2 g10171.t2 PANTHER PTHR11652:SF60 28S RIBOSOMAL PROTEIN S12, MITOCHONDRIAL 12 136 1.5E-58
3 g10171.t2 PANTHER PTHR11652 30S RIBOSOMAL PROTEIN S12 FAMILY MEMBER 12 136 1.5E-58
5 g10171.t2 PRINTS PR01034 Ribosomal protein S12 signature 52 67 3.4E-28
4 g10171.t2 PRINTS PR01034 Ribosomal protein S12 signature 67 82 3.4E-28
6 g10171.t2 PRINTS PR01034 Ribosomal protein S12 signature 83 102 3.4E-28
8 g10171.t2 PRINTS PR01034 Ribosomal protein S12 signature 102 119 3.4E-28
7 g10171.t2 PRINTS PR01034 Ribosomal protein S12 signature 119 135 3.4E-28
1 g10171.t2 Pfam PF00164 Ribosomal protein S12/S23 47 129 1.4E-23
12 g10171.t2 ProSitePatterns PS00055 Ribosomal protein S12 signature. 68 75 -
9 g10171.t2 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 32 135 5.4E-37
13 g10171.t2 TIGRFAM TIGR00981 rpsL_bact: ribosomal protein uS12 29 135 1.3E-33

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
GO:0015935 small ribosomal subunit CC

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.

Raw TPM values