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.t93 TSS g13143.t93 28151119 28151119
chr_1 g13143 g13143.t93 isoform g13143.t93 28151137 28152591
chr_1 g13143 g13143.t93 exon g13143.t93.exon1 28151137 28151139
chr_1 g13143 g13143.t93 cds g13143.t93.CDS1 28151137 28151139
chr_1 g13143 g13143.t93 exon g13143.t93.exon2 28151209 28151467
chr_1 g13143 g13143.t93 cds g13143.t93.CDS2 28151209 28151467
chr_1 g13143 g13143.t93 exon g13143.t93.exon3 28151695 28151792
chr_1 g13143 g13143.t93 cds g13143.t93.CDS3 28151695 28151792
chr_1 g13143 g13143.t93 exon g13143.t93.exon4 28152163 28152478
chr_1 g13143 g13143.t93 cds g13143.t93.CDS4 28152163 28152478
chr_1 g13143 g13143.t93 exon g13143.t93.exon5 28152543 28152591
chr_1 g13143 g13143.t93 cds g13143.t93.CDS5 28152543 28152589
chr_1 g13143 g13143.t93 TTS g13143.t93 28152716 28152716

Sequences

>g13143.t93 Gene=g13143 Length=725
ATGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGCAGCTCCAAAAGCATGGATGCTG
GACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAACCGGTCCTCATAAATTGCGTGAA
TCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAAGTATGCTTTGACCAACACTGAA
ACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGATGGAAAAGTCAGAACAGATATC
AATTATCCAGCAGGTTTCATGGATGTCATCACCATTGAGAAAACTGGTGAATTCTTCCGT
TTGATCTATGATGTAAAGGGTCGTTTTACAATCCATCGCATTACTGCCGATGAAGCAAAA
TACAAGTTATGCAAAGTGAAGCGTGTAACAATTGGACCTAAGAAGATTCCATACTTGGTC
ACACATGATGGTCGTACACTCCGTTATCCAGATCCAAACATTCATGTAAACGACACAATT
CAATTAGATATTGCAACTGGAAAAATCACAGATCATATTCGTTTTGAATCCGGCAATTTG
GTTATGGTTACTGGAGGTCGTAACTTGGGTCGAGTTGGTACTGTTGTGAATCGTGAAAAG
CATCCTGGTTCATTTGAAATCATTCATGTGAAAGACGCTAATGGACATATGTTTGCTACT
CGTTTGACAAACATTTTGTTGCCGAAGAACGCGATAAGCGATTGGCACAAAAAACCACTA
ACTAA

>g13143.t93 Gene=g13143 Length=241
MARGPKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTE
TKKIVMQRHIKVDGKVRTDINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAK
YKLCKVKRVTIGPKKIPYLVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFESGNL
VMVTGGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMFATRLTNILLPKNAISDWHKKPL
T

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g13143.t93 CDD cd00165 S4 44 112 1.36585E-6
13 g13143.t93 CDD cd06087 KOW_RPS4 175 225 6.86204E-26
9 g13143.t93 Gene3D G3DSA:3.10.290.40 - 1 117 7.7E-61
11 g13143.t93 Gene3D G3DSA:2.40.50.740 - 122 172 5.7E-29
10 g13143.t93 Gene3D G3DSA:2.30.30.30 - 175 237 5.8E-25
7 g13143.t93 Hamap MF_00485 30S ribosomal protein S4e [rps4e]. 7 234 34.714703
5 g13143.t93 PANTHER PTHR11581:SF33 40S RIBOSOMAL PROTEIN S4 2 228 1.4E-124
6 g13143.t93 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 2 228 1.4E-124
12 g13143.t93 PIRSF PIRSF002116 RPS4a_RPS4e 1 238 5.9E-96
1 g13143.t93 Pfam PF08071 RS4NT (NUC023) domain 3 39 7.2E-20
3 g13143.t93 Pfam PF01479 S4 domain 43 90 1.2E-9
4 g13143.t93 Pfam PF00900 Ribosomal family S4e 95 169 2.8E-36
2 g13143.t93 Pfam PF00467 KOW motif 178 210 3.7E-6
17 g13143.t93 ProSitePatterns PS00528 Ribosomal protein S4e signature. 8 22 -
18 g13143.t93 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 42 105 10.755
15 g13143.t93 SMART SM00363 s4_6 42 106 2.2E-4
16 g13143.t93 SMART SM00739 kow_9 174 201 0.0023
8 g13143.t93 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 51 135 1.96E-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