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.t18 TSS g13143.t18 28150713 28150713
chr_1 g13143 g13143.t18 isoform g13143.t18 28150723 28152591
chr_1 g13143 g13143.t18 exon g13143.t18.exon1 28150723 28150735
chr_1 g13143 g13143.t18 exon g13143.t18.exon2 28151120 28151139
chr_1 g13143 g13143.t18 cds g13143.t18.CDS1 28151137 28151139
chr_1 g13143 g13143.t18 exon g13143.t18.exon3 28151209 28151467
chr_1 g13143 g13143.t18 cds g13143.t18.CDS2 28151209 28151467
chr_1 g13143 g13143.t18 exon g13143.t18.exon4 28151695 28151792
chr_1 g13143 g13143.t18 cds g13143.t18.CDS3 28151695 28151792
chr_1 g13143 g13143.t18 exon g13143.t18.exon5 28152163 28152232
chr_1 g13143 g13143.t18 cds g13143.t18.CDS4 28152163 28152232
chr_1 g13143 g13143.t18 exon g13143.t18.exon6 28152359 28152591
chr_1 g13143 g13143.t18 cds g13143.t18.CDS5 28152359 28152591
chr_1 g13143 g13143.t18 TTS g13143.t18 28152716 28152716

Sequences

>g13143.t18 Gene=g13143 Length=693
TTGTCAATCCTAAGTAATTAACTTTGGGAAATGGCTCGCGGTCCGAAAAAACATTTGAAG
CGTTTAGCAGCTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGT
CCATCAACCGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAAT
CGCTTGAAGTATGCTTTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATC
AAAGTTGATGGAAAAGTCAGAACAGATATCAATTATCCAGCAGGTTTCATGGATGTCATC
ACCATTGAGAAAACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACA
ATCCATCGCATTACTGCCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGCGTGTAACA
ATTGGACCTAAGAAGATTCCATACTTGGTCACACATGATGGTCGTAACTTGGGTCGAGTT
GGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTGAAAGAC
GCTAATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAAGGCGCA
AAGGCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAAGAACGC
GATAAGCGATTGGCACAAAAAACCACTAACTAA

>g13143.t18 Gene=g13143 Length=220
MARGPKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTE
TKKIVMQRHIKVDGKVRTDINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAK
YKLCKVKRVTIGPKKIPYLVTHDGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMFATRL
TNIFIIGKGAKAYISLPKGKGIKLSVAEERDKRLAQKTTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g13143.t18 CDD cd00165 S4 44 112 2.29393E-6
14 g13143.t18 CDD cd06087 KOW_RPS4 143 187 9.19125E-22
10 g13143.t18 Gene3D G3DSA:3.10.290.40 - 1 117 6.1E-61
11 g13143.t18 Gene3D G3DSA:2.30.30.30 - 137 203 1.2E-29
6 g13143.t18 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 1 146 2.4E-109
8 g13143.t18 PANTHER PTHR11581:SF8 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1 1 146 2.4E-109
5 g13143.t18 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 144 217 2.4E-109
7 g13143.t18 PANTHER PTHR11581:SF8 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1 144 217 2.4E-109
12 g13143.t18 PIRSF PIRSF002116 RPS4a_RPS4e 1 147 1.1E-66
13 g13143.t18 PIRSF PIRSF002116 RPS4a_RPS4e 143 199 2.6E-12
1 g13143.t18 Pfam PF08071 RS4NT (NUC023) domain 3 39 6.2E-20
2 g13143.t18 Pfam PF01479 S4 domain 43 90 1.1E-9
4 g13143.t18 Pfam PF00900 Ribosomal family S4e 95 147 6.4E-25
3 g13143.t18 Pfam PF16121 40S ribosomal protein S4 C-terminus 170 217 4.7E-26
16 g13143.t18 ProSitePatterns PS00528 Ribosomal protein S4e signature. 8 22 -
18 g13143.t18 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 42 105 10.755
17 g13143.t18 SMART SM00363 s4_6 42 106 2.2E-4
9 g13143.t18 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 51 133 9.64E-7

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

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