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.t22 TSS g13143.t22 28150713 28150713
chr_1 g13143 g13143.t22 isoform g13143.t22 28150723 28152591
chr_1 g13143 g13143.t22 exon g13143.t22.exon1 28150723 28150739
chr_1 g13143 g13143.t22 exon g13143.t22.exon2 28151200 28151363
chr_1 g13143 g13143.t22 cds g13143.t22.CDS1 28151260 28151363
chr_1 g13143 g13143.t22 exon g13143.t22.exon3 28151409 28151467
chr_1 g13143 g13143.t22 cds g13143.t22.CDS2 28151409 28151467
chr_1 g13143 g13143.t22 exon g13143.t22.exon4 28151695 28151792
chr_1 g13143 g13143.t22 cds g13143.t22.CDS3 28151695 28151792
chr_1 g13143 g13143.t22 exon g13143.t22.exon5 28152163 28152591
chr_1 g13143 g13143.t22 cds g13143.t22.CDS4 28152163 28152591
chr_1 g13143 g13143.t22 TTS g13143.t22 28152716 28152716

Sequences

>g13143.t22 Gene=g13143 Length=767
TTGTCAATCCTAAGTAATGATTGTAGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAG
CAGCTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAA
CCGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGA
AACACATCAAAGTTGATGGAAAAGTCAGAACAGATATCAATTATCCAGCAGGTTTCATGG
ATGTCATCACCATTGAGAAAACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTC
GTTTTACAATCCATCGCATTACTGCCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGC
GTGTAACAATTGGACCTAAGAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCC
GTTATCCAGATCCAAACATTCATGTAAACGACACAATTCAATTAGATATTGCAACTGGAA
AAATCACAGATCATATTCGTTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTA
ACTTGGGTCGAGTTGGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCA
TTCATGTGAAAGACGCTAATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCA
TCGGAAAAGGCGCAAAGGCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTG
TTGCCGAAGAACGCGATAAGCGATTGGCACAAAAAACCACTAACTAA

>g13143.t22 Gene=g13143 Length=229
MLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKHIKVDGKVRTDINYPAGFMDVITIE
KTGEFFRLIYDVKGRFTIHRITADEAKYKLCKVKRVTIGPKKIPYLVTHDGRTLRYPDPN
IHVNDTIQLDIATGKITDHIRFESGNLVMVTGGRNLGRVGTVVNREKHPGSFEIIHVKDA
NGHMFATRLTNIFIIGKGAKAYISLPKGKGIKLSVAEERDKRLAQKTTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g13143.t22 CDD cd06087 KOW_RPS4 142 196 0.0e+00
9 g13143.t22 Gene3D G3DSA:3.10.290.40 - 1 35 0.0e+00
8 g13143.t22 Gene3D G3DSA:3.10.290.40 - 36 84 0.0e+00
11 g13143.t22 Gene3D G3DSA:2.40.50.740 - 89 139 0.0e+00
10 g13143.t22 Gene3D G3DSA:2.30.30.30 - 142 212 0.0e+00
5 g13143.t22 PANTHER PTHR11581:SF30 40S RIBOSOMAL PROTEIN S4, X ISOFORM 1 226 0.0e+00
6 g13143.t22 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 1 226 0.0e+00
12 g13143.t22 PIRSF PIRSF002116 RPS4a_RPS4e 1 208 0.0e+00
1 g13143.t22 Pfam PF08071 RS4NT (NUC023) domain 1 21 1.0e-07
4 g13143.t22 Pfam PF00900 Ribosomal family S4e 62 136 0.0e+00
2 g13143.t22 Pfam PF00467 KOW motif 145 177 3.4e-06
3 g13143.t22 Pfam PF16121 40S ribosomal protein S4 C-terminus 179 226 0.0e+00
7 g13143.t22 SMART SM00739 kow_9 141 168 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.

Raw TPM values