Gene loci information

Transcript annotation

  • This transcript has been annotated as 28S ribosomal protein S2, 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 g13624 g13624.t3 TTS g13624.t3 31340018 31340018
chr_1 g13624 g13624.t3 isoform g13624.t3 31340054 31340842
chr_1 g13624 g13624.t3 exon g13624.t3.exon1 31340054 31340842
chr_1 g13624 g13624.t3 cds g13624.t3.CDS1 31340067 31340813
chr_1 g13624 g13624.t3 TSS g13624.t3 31340987 31340987

Sequences

>g13624.t3 Gene=g13624 Length=789
AAGGATTATTGCGTATTATAGCAAATAATATGACAAAAAAGAATTTTTCATCCGCAACAG
CGCCTGCATTAGAAATTGAGCCAAAAAAAGATGTTGAAGTACCAACAAAAATTAGTCGAA
TTAATCCATTAACTCATCCAGATTATTTTGGCGTTGGAAAAATGTTTACAGTTCGCGATT
TAATGGAAGCTCGTGTACATTTCGGTCACAAGGATGGATCTTTGAATGATAGAATGAAAC
CCTATTTATTTGGATCGCGATTAAATCACACAATATTCAATCTTGATATAACTGCAGAAC
ATTTAAAGAGAGCTCTTAATGTAACTGCACATACGGCATTGCAAGGTGGTCTCATTCTCT
TTTTCTGTCGCAGTTCAATCAATGCACATACTGTAGAGAAAACTGCAAAAGAATGTGGTG
AATTTGCTCACACGAGATATTGGAGAGGAGGAACATTTACAAACTCAAAAATTCAATTTA
AAGCTATCACACGACTTCCAGATTTATGCATCTTTCTTAATACACTCAACAATGTTATGC
TACAACATACAGCAGTTCGAGATGCAGCTAAAATGAATATTCCTTCAATTGGTATTGTTG
ATAGCAATTGTTCACCAGATTTAATCACTTATCTTGTACCAGGAAATGACGATTCTCCTG
CATCTATTGAACTTTATTGTTCACTCTTTAAAGAAGCAATTTTAAGAGGAAAAGCTAAAC
GAAAAGAACTCTTGCAAGAAATTGAAAATATGGAAAAAGAACAGAAAGATTCTTAGAATT
AACTTAAAG

>g13624.t3 Gene=g13624 Length=248
MTKKNFSSATAPALEIEPKKDVEVPTKISRINPLTHPDYFGVGKMFTVRDLMEARVHFGH
KDGSLNDRMKPYLFGSRLNHTIFNLDITAEHLKRALNVTAHTALQGGLILFFCRSSINAH
TVEKTAKECGEFAHTRYWRGGTFTNSKIQFKAITRLPDLCIFLNTLNNVMLQHTAVRDAA
KMNIPSIGIVDSNCSPDLITYLVPGNDDSPASIELYCSLFKEAILRGKAKRKELLQEIEN
MEKEQKDS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13624.t3 CDD cd01425 RPS2 51 226 1.81053E-69
10 g13624.t3 Coils Coil Coil 224 248 -
9 g13624.t3 Gene3D G3DSA:3.40.50.10490 - 42 230 2.7E-64
3 g13624.t3 Hamap MF_00291_B 30S ribosomal protein S2 [rpsB]. 44 228 15.66165
2 g13624.t3 PANTHER PTHR12534 30S RIBOSOMAL PROTEIN S2 PROKARYOTIC AND ORGANELLAR 36 232 2.0E-62
5 g13624.t3 PRINTS PR00395 Ribosomal protein S2 signature 48 66 2.8E-13
7 g13624.t3 PRINTS PR00395 Ribosomal protein S2 signature 129 146 2.8E-13
6 g13624.t3 PRINTS PR00395 Ribosomal protein S2 signature 178 189 2.8E-13
4 g13624.t3 PRINTS PR00395 Ribosomal protein S2 signature 199 213 2.8E-13
1 g13624.t3 Pfam PF00318 Ribosomal protein S2 51 155 2.3E-22
12 g13624.t3 ProSitePatterns PS00962 Ribosomal protein S2 signature 1. 48 59 -
8 g13624.t3 SUPERFAMILY SSF52313 Ribosomal protein S2 48 235 2.49E-55
13 g13624.t3 TIGRFAM TIGR01011 rpsB_bact: ribosomal protein uS2 46 159 2.5E-22

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