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.t87 TSS g13143.t87 28150713 28150713
chr_1 g13143 g13143.t87 isoform g13143.t87 28150731 28161163
chr_1 g13143 g13143.t87 exon g13143.t87.exon1 28150731 28150735
chr_1 g13143 g13143.t87 exon g13143.t87.exon2 28151120 28151139
chr_1 g13143 g13143.t87 cds g13143.t87.CDS1 28151137 28151139
chr_1 g13143 g13143.t87 exon g13143.t87.exon3 28151209 28151467
chr_1 g13143 g13143.t87 cds g13143.t87.CDS2 28151209 28151467
chr_1 g13143 g13143.t87 exon g13143.t87.exon4 28151695 28151792
chr_1 g13143 g13143.t87 cds g13143.t87.CDS3 28151695 28151792
chr_1 g13143 g13143.t87 exon g13143.t87.exon5 28152163 28152704
chr_1 g13143 g13143.t87 cds g13143.t87.CDS4 28152163 28152591
chr_1 g13143 g13143.t87 exon g13143.t87.exon6 28161149 28161163
chr_1 g13143 g13143.t87 TTS g13143.t87 NA NA

Sequences

>g13143.t87 Gene=g13143 Length=939
CCTAAGTAATTAACTTTGGGAAATGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGC
AGCTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAAC
CGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAA
GTATGCTTTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGA
TGGAAAAGTCAGAACAGATATCAATTATCCAGCAGGTTTCATGGATGTCATCACCATTGA
GAAAACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACAATCCATCG
CATTACTGCCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGCGTGTAACAATTGGACC
TAAGAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCCAGATCCAAA
CATTCATGTAAACGACACAATTCAATTAGATATTGCAACTGGAAAAATCACAGATCATAT
TCGTTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGGTCGAGTTGG
TACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTGAAAGACGC
TAATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAAGGCGCAAA
GGCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAAGAACGCGA
TAAGCGATTGGCACAAAAAACCACTAACTAAGAGACGAAAGCTATTGTGTTAAGAAAGAA
CAGCTTTTAAGAGGAGGACAGTGAATGCAAGAATAACTGCGAGAAAATGAGAATATAATG
AAATTCCTTCATTAATAAATAAAAATTTCATAAAAGCGA

>g13143.t87 Gene=g13143 Length=262
MARGPKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTE
TKKIVMQRHIKVDGKVRTDINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAK
YKLCKVKRVTIGPKKIPYLVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFESGNL
VMVTGGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMFATRLTNIFIIGKGAKAYISLPK
GKGIKLSVAEERDKRLAQKTTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g13143.t87 CDD cd00165 S4 44 112 2.40616E-6
14 g13143.t87 CDD cd06087 KOW_RPS4 175 229 1.60299E-28
10 g13143.t87 Gene3D G3DSA:3.10.290.40 - 1 117 9.4E-61
12 g13143.t87 Gene3D G3DSA:2.40.50.740 - 122 172 6.5E-29
11 g13143.t87 Gene3D G3DSA:2.30.30.30 - 175 245 4.2E-36
8 g13143.t87 Hamap MF_00485 30S ribosomal protein S4e [rps4e]. 7 238 36.502556
6 g13143.t87 PANTHER PTHR11581:SF30 40S RIBOSOMAL PROTEIN S4, X ISOFORM 1 259 2.7E-138
7 g13143.t87 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 1 259 2.7E-138
13 g13143.t87 PIRSF PIRSF002116 RPS4a_RPS4e 1 241 8.6E-100
1 g13143.t87 Pfam PF08071 RS4NT (NUC023) domain 3 39 8.1E-20
3 g13143.t87 Pfam PF01479 S4 domain 43 90 1.4E-9
5 g13143.t87 Pfam PF00900 Ribosomal family S4e 95 169 3.3E-36
2 g13143.t87 Pfam PF00467 KOW motif 178 210 4.2E-6
4 g13143.t87 Pfam PF16121 40S ribosomal protein S4 C-terminus 212 259 6.3E-26
18 g13143.t87 ProSitePatterns PS00528 Ribosomal protein S4e signature. 8 22 -
19 g13143.t87 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 42 105 10.755
16 g13143.t87 SMART SM00363 s4_6 42 106 2.2E-4
17 g13143.t87 SMART SM00739 kow_9 174 201 0.0023
9 g13143.t87 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 51 134 2.36E-6

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

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