Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 40S ribosomal protein S15.

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 g11431 g11431.t14 isoform g11431.t14 16195311 16196344
chr_1 g11431 g11431.t14 exon g11431.t14.exon1 16195311 16195318
chr_1 g11431 g11431.t14 exon g11431.t14.exon2 16195528 16195576
chr_1 g11431 g11431.t14 cds g11431.t14.CDS1 16195568 16195576
chr_1 g11431 g11431.t14 exon g11431.t14.exon3 16195640 16195951
chr_1 g11431 g11431.t14 cds g11431.t14.CDS2 16195640 16195951
chr_1 g11431 g11431.t14 exon g11431.t14.exon4 16196219 16196344
chr_1 g11431 g11431.t14 cds g11431.t14.CDS3 16196219 16196344
chr_1 g11431 g11431.t14 TTS g11431.t14 16196443 16196443
chr_1 g11431 g11431.t14 TSS g11431.t14 NA NA

Sequences

>g11431.t14 Gene=g11431 Length=495
TTGATCAGTTTATTTTAGAGTTCGTGAAATAATTGTGTTATCGAAATCATGGCTGATGCT
CAAGAAGAACAAGTTCGCAAGAAGCGTACCTTCCGTAAATTTACATATCGTGGAGTTGAT
TTAGATCAACTTTTGGATATGCCAAATGAACAACTCTCAGAGTTGATGCATAGTCGTGCT
CGTCGTCGTTTTGCTCGTGGATTGAAACGCAAACCAATGGCTTTAATCCAAAAGTTGCGA
AAGGCAAAGAAAGAGGCACCTCCACTTGAGAAGCCAGCTATTGTTAAGACTCATTTGCGT
GACATGATCATTGTACCCGAAATGGTTGGATCAATCGTCGGTATCTATAATGGAAAAACA
TTCAATCAAGTTGAAATCAAGCCAGAAATGATTGGACACTATTTAGGAGACTTTTCGCTC
ACATATAAACCAGTTAAGCATGGTCGTCCCGGTATTGGTGCCACGCACAGTTCACGATTT
ATTCCATTAAAGTAA

>g11431.t14 Gene=g11431 Length=148
MADAQEEQVRKKRTFRKFTYRGVDLDQLLDMPNEQLSELMHSRARRRFARGLKRKPMALI
QKLRKAKKEAPPLEKPAIVKTHLRDMIIVPEMVGSIVGIYNGKTFNQVEIKPEMIGHYLG
DFSLTYKPVKHGRPGIGATHSSRFIPLK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11431.t14 Gene3D G3DSA:3.30.860.20 - 4 148 1.7E-73
4 g11431.t14 Hamap MF_00531 30S ribosomal protein S19 [rpsS]. 44 137 21.446079
2 g11431.t14 PANTHER PTHR11880 RIBOSOMAL PROTEIN S19P FAMILY MEMBER 3 148 5.8E-79
3 g11431.t14 PANTHER PTHR11880:SF2 40S RIBOSOMAL PROTEIN S15 3 148 5.8E-79
10 g11431.t14 PIRSF PIRSF002144 RPS19p_RPS19a_RPS15e_RPS19o 1 148 3.3E-41
7 g11431.t14 PRINTS PR00975 Ribosomal protein S19 family signature 81 100 6.8E-14
5 g11431.t14 PRINTS PR00975 Ribosomal protein S19 family signature 101 113 6.8E-14
6 g11431.t14 PRINTS PR00975 Ribosomal protein S19 family signature 113 128 6.8E-14
1 g11431.t14 Pfam PF00203 Ribosomal protein S19 46 131 4.6E-34
11 g11431.t14 ProSitePatterns PS00323 Ribosomal protein S19 signature. 101 125 -
8 g11431.t14 SUPERFAMILY SSF54570 Ribosomal protein S19 52 132 1.01E-30
12 g11431.t14 TIGRFAM TIGR01025 uS19_arch: ribosomal protein uS19 15 148 5.1E-68

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:0003723 RNA binding MF
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