Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S4.

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 g13143 g13143.t37 TSS g13143.t37 28150713 28150713
chr_1 g13143 g13143.t37 isoform g13143.t37 28150723 28152591
chr_1 g13143 g13143.t37 exon g13143.t37.exon1 28150723 28150739
chr_1 g13143 g13143.t37 exon g13143.t37.exon2 28151209 28151467
chr_1 g13143 g13143.t37 cds g13143.t37.CDS1 28151423 28151467
chr_1 g13143 g13143.t37 exon g13143.t37.exon3 28151712 28151792
chr_1 g13143 g13143.t37 cds g13143.t37.CDS2 28151712 28151792
chr_1 g13143 g13143.t37 exon g13143.t37.exon4 28152163 28152591
chr_1 g13143 g13143.t37 cds g13143.t37.CDS3 28152163 28152591
chr_1 g13143 g13143.t37 TTS g13143.t37 28152716 28152716

Sequences

>g13143.t37 Gene=g13143 Length=786
TTGTCAATCCTAAGTAAGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGCAGCTCCAA
AAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAACCGGTCCTC
ATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAAGTATGCTT
TGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGATGGAAAAG
TCAGAACAGATATCAATTATCCAGCAGGTTTCATGGAAAACTGGTGAATTCTTCCGTTTG
ATCTATGATGTAAAGGGTCGTTTTACAATCCATCGCATTACTGCCGATGAAGCAAAATAC
AAGTTATGCAAAGTGAAGCGTGTAACAATTGGACCTAAGAAGATTCCATACTTGGTCACA
CATGATGGTCGTACACTCCGTTATCCAGATCCAAACATTCATGTAAACGACACAATTCAA
TTAGATATTGCAACTGGAAAAATCACAGATCATATTCGTTTTGAATCCGGCAATTTGGTT
ATGGTTACTGGAGGTCGTAACTTGGGTCGAGTTGGTACTGTTGTGAATCGTGAAAAGCAT
CCTGGTTCATTTGAAATCATTCATGTGAAAGACGCTAATGGACATATGTTTGCTACTCGT
TTGACAAACATTTTCATCATCGGAAAAGGCGCAAAGGCATACATTTCATTGCCTAAAGGC
AAGGGTATTAAACTCAGTGTTGCCGAAGAACGCGATAAGCGATTGGCACAAAAAACCACT
AACTAA

>g13143.t37 Gene=g13143 Length=184
MEKSEQISIIQQVSWKTGEFFRLIYDVKGRFTIHRITADEAKYKLCKVKRVTIGPKKIPY
LVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFESGNLVMVTGGRNLGRVGTVVNR
EKHPGSFEIIHVKDANGHMFATRLTNIFIIGKGAKAYISLPKGKGIKLSVAEERDKRLAQ
KTTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13143.t37 CDD cd06087 KOW_RPS4 97 151 0.0e+00
7 g13143.t37 Gene3D G3DSA:2.40.50.740 - 44 94 0.0e+00
6 g13143.t37 Gene3D G3DSA:2.30.30.30 - 97 167 0.0e+00
4 g13143.t37 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 16 179 0.0e+00
3 g13143.t37 Pfam PF00900 Ribosomal family S4e 17 91 0.0e+00
1 g13143.t37 Pfam PF00467 KOW motif 100 132 2.5e-06
2 g13143.t37 Pfam PF16121 40S ribosomal protein S4 C-terminus 134 181 0.0e+00
5 g13143.t37 SMART SM00739 kow_9 96 123 2.3e-03

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

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. There were no conditions that were differentially expressed