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.t19 isoform g11431.t19 16195438 16196344
chr_1 g11431 g11431.t19 exon g11431.t19.exon1 16195438 16195441
chr_1 g11431 g11431.t19 exon g11431.t19.exon2 16195608 16195951
chr_1 g11431 g11431.t19 cds g11431.t19.CDS1 16195721 16195951
chr_1 g11431 g11431.t19 exon g11431.t19.exon3 16196219 16196344
chr_1 g11431 g11431.t19 cds g11431.t19.CDS2 16196219 16196344
chr_1 g11431 g11431.t19 TTS g11431.t19 16196443 16196443
chr_1 g11431 g11431.t19 TSS g11431.t19 NA NA

Sequences

>g11431.t19 Gene=g11431 Length=474
TCTTGATTAAAATAATAGTGAAAATATTTTTTTCAGGCTCAAGAAGAACAAGTTCGCAAG
AAGCGTACCTTCCGTAAATTTACATATCGTGGAGTTGATTTAGATCAACTTTTGGATATG
CCAAATGAACAACTCTCAGAGTTGATGCATAGTCGTGCTCGTCGTCGTTTTGCTCGTGGA
TTGAAACGCAAACCAATGGCTTTAATCCAAAAGTTGCGAAAGGCAAAGAAAGAGGCACCT
CCACTTGAGAAGCCAGCTATTGTTAAGACTCATTTGCGTGACATGATCATTGTACCCGAA
ATGGTTGGATCAATCGTCGGTATCTATAATGGAAAAACATTCAATCAAGTTGAAATCAAG
CCAGAAATGATTGGACACTATTTAGGAGACTTTTCGCTCACATATAAACCAGTTAAGCAT
GGTCGTCCCGGTATTGGTGCCACGCACAGTTCACGATTTATTCCATTAAAGTAA

>g11431.t19 Gene=g11431 Length=118
MPNEQLSELMHSRARRRFARGLKRKPMALIQKLRKAKKEAPPLEKPAIVKTHLRDMIIVP
EMVGSIVGIYNGKTFNQVEIKPEMIGHYLGDFSLTYKPVKHGRPGIGATHSSRFIPLK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11431.t19 Gene3D G3DSA:3.30.860.20 - 1 118 4.3E-60
4 g11431.t19 Hamap MF_00531 30S ribosomal protein S19 [rpsS]. 14 107 21.446079
2 g11431.t19 PANTHER PTHR11880:SF50 LOW QUALITY PROTEIN: 40S RIBOSOMAL PROTEIN S15 2 118 1.6E-64
3 g11431.t19 PANTHER PTHR11880 RIBOSOMAL PROTEIN S19P FAMILY MEMBER 2 118 1.6E-64
10 g11431.t19 PIRSF PIRSF002144 RPS19p_RPS19a_RPS15e_RPS19o 5 118 1.6E-37
7 g11431.t19 PRINTS PR00975 Ribosomal protein S19 family signature 51 70 4.4E-14
5 g11431.t19 PRINTS PR00975 Ribosomal protein S19 family signature 71 83 4.4E-14
6 g11431.t19 PRINTS PR00975 Ribosomal protein S19 family signature 83 98 4.4E-14
1 g11431.t19 Pfam PF00203 Ribosomal protein S19 16 101 2.3E-34
11 g11431.t19 ProSitePatterns PS00323 Ribosomal protein S19 signature. 71 95 -
8 g11431.t19 SUPERFAMILY SSF54570 Ribosomal protein S19 22 102 5.1E-31
12 g11431.t19 TIGRFAM TIGR01025 uS19_arch: ribosomal protein uS19 1 118 4.2E-59

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

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