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.t1 TTS g13624.t1 31340018 31340018
chr_1 g13624 g13624.t1 isoform g13624.t1 31340067 31340925
chr_1 g13624 g13624.t1 exon g13624.t1.exon1 31340067 31340845
chr_1 g13624 g13624.t1 cds g13624.t1.CDS1 31340067 31340845
chr_1 g13624 g13624.t1 exon g13624.t1.exon2 31340907 31340925
chr_1 g13624 g13624.t1 cds g13624.t1.CDS2 31340907 31340925
chr_1 g13624 g13624.t1 TSS g13624.t1 31340987 31340987

Sequences

>g13624.t1 Gene=g13624 Length=798
ATGCTTTTAAAAGGACAAGGACAAGGATTATTGCGTATTATAGCAAATAATATGACAAAA
AAGAATTTTTCATCCGCAACAGCGCCTGCATTAGAAATTGAGCCAAAAAAAGATGTTGAA
GTACCAACAAAAATTAGTCGAATTAATCCATTAACTCATCCAGATTATTTTGGCGTTGGA
AAAATGTTTACAGTTCGCGATTTAATGGAAGCTCGTGTACATTTCGGTCACAAGGATGGA
TCTTTGAATGATAGAATGAAACCCTATTTATTTGGATCGCGATTAAATCACACAATATTC
AATCTTGATATAACTGCAGAACATTTAAAGAGAGCTCTTAATGTAACTGCACATACGGCA
TTGCAAGGTGGTCTCATTCTCTTTTTCTGTCGCAGTTCAATCAATGCACATACTGTAGAG
AAAACTGCAAAAGAATGTGGTGAATTTGCTCACACGAGATATTGGAGAGGAGGAACATTT
ACAAACTCAAAAATTCAATTTAAAGCTATCACACGACTTCCAGATTTATGCATCTTTCTT
AATACACTCAACAATGTTATGCTACAACATACAGCAGTTCGAGATGCAGCTAAAATGAAT
ATTCCTTCAATTGGTATTGTTGATAGCAATTGTTCACCAGATTTAATCACTTATCTTGTA
CCAGGAAATGACGATTCTCCTGCATCTATTGAACTTTATTGTTCACTCTTTAAAGAAGCA
ATTTTAAGAGGAAAAGCTAAACGAAAAGAACTCTTGCAAGAAATTGAAAATATGGAAAAA
GAACAGAAAGATTCTTAG

>g13624.t1 Gene=g13624 Length=265
MLLKGQGQGLLRIIANNMTKKNFSSATAPALEIEPKKDVEVPTKISRINPLTHPDYFGVG
KMFTVRDLMEARVHFGHKDGSLNDRMKPYLFGSRLNHTIFNLDITAEHLKRALNVTAHTA
LQGGLILFFCRSSINAHTVEKTAKECGEFAHTRYWRGGTFTNSKIQFKAITRLPDLCIFL
NTLNNVMLQHTAVRDAAKMNIPSIGIVDSNCSPDLITYLVPGNDDSPASIELYCSLFKEA
ILRGKAKRKELLQEIENMEKEQKDS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13624.t1 CDD cd01425 RPS2 68 243 7.40765E-69
10 g13624.t1 Coils Coil Coil 241 265 -
9 g13624.t1 Gene3D G3DSA:3.40.50.10490 - 59 247 3.4E-64
3 g13624.t1 Hamap MF_00291_B 30S ribosomal protein S2 [rpsB]. 61 245 15.66165
2 g13624.t1 PANTHER PTHR12534 30S RIBOSOMAL PROTEIN S2 PROKARYOTIC AND ORGANELLAR 53 248 2.5E-62
4 g13624.t1 PRINTS PR00395 Ribosomal protein S2 signature 65 83 3.5E-13
6 g13624.t1 PRINTS PR00395 Ribosomal protein S2 signature 146 163 3.5E-13
7 g13624.t1 PRINTS PR00395 Ribosomal protein S2 signature 195 206 3.5E-13
5 g13624.t1 PRINTS PR00395 Ribosomal protein S2 signature 216 230 3.5E-13
1 g13624.t1 Pfam PF00318 Ribosomal protein S2 68 172 2.7E-22
12 g13624.t1 ProSitePatterns PS00962 Ribosomal protein S2 signature 1. 65 76 -
8 g13624.t1 SUPERFAMILY SSF52313 Ribosomal protein S2 65 252 3.14E-55
13 g13624.t1 TIGRFAM TIGR01011 rpsB_bact: ribosomal protein uS2 63 176 3.0E-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