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.t26 TSS g13143.t26 28150713 28150713
chr_1 g13143 g13143.t26 isoform g13143.t26 28150723 28152591
chr_1 g13143 g13143.t26 exon g13143.t26.exon1 28150723 28150739
chr_1 g13143 g13143.t26 exon g13143.t26.exon2 28151246 28151467
chr_1 g13143 g13143.t26 cds g13143.t26.CDS1 28151260 28151467
chr_1 g13143 g13143.t26 exon g13143.t26.exon3 28151695 28151792
chr_1 g13143 g13143.t26 cds g13143.t26.CDS2 28151695 28151792
chr_1 g13143 g13143.t26 exon g13143.t26.exon4 28152163 28152591
chr_1 g13143 g13143.t26 cds g13143.t26.CDS3 28152163 28152591
chr_1 g13143 g13143.t26 TTS g13143.t26 28152716 28152716

Sequences

>g13143.t26 Gene=g13143 Length=766
TTGTCAATCCTAAGTAACTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGC
TCCTCGTCCATCAACCGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTT
GCGCAATCGCTTGAAGTATGCTTTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAG
ACACATCAAAGTTGATGGAAAAGTCAGAACAGATATCAATTATCCAGCAGGTTTCATGGA
TGTCATCACCATTGAGAAAACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCG
TTTTACAATCCATCGCATTACTGCCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGCG
TGTAACAATTGGACCTAAGAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCG
TTATCCAGATCCAAACATTCATGTAAACGACACAATTCAATTAGATATTGCAACTGGAAA
AATCACAGATCATATTCGTTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAA
CTTGGGTCGAGTTGGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCAT
TCATGTGAAAGACGCTAATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCAT
CGGAAAAGGCGCAAAGGCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGT
TGCCGAAGAACGCGATAAGCGATTGGCACAAAAAACCACTAACTAA

>g13143.t26 Gene=g13143 Length=244
MLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTETKKIVMQRHIKVDGKVRT
DINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAKYKLCKVKRVTIGPKKIPY
LVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFESGNLVMVTGGRNLGRVGTVVNR
EKHPGSFEIIHVKDANGHMFATRLTNIFIIGKGAKAYISLPKGKGIKLSVAEERDKRLAQ
KTTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g13143.t26 CDD cd00165 S4 26 94 0.0000027
14 g13143.t26 CDD cd06087 KOW_RPS4 157 211 0.0000000
10 g13143.t26 Gene3D G3DSA:3.10.290.40 - 1 99 0.0000000
12 g13143.t26 Gene3D G3DSA:2.40.50.740 - 104 154 0.0000000
11 g13143.t26 Gene3D G3DSA:2.30.30.30 - 157 227 0.0000000
8 g13143.t26 Hamap MF_00485 30S ribosomal protein S4e [rps4e]. 3 220 30.2717490
6 g13143.t26 PANTHER PTHR11581:SF30 40S RIBOSOMAL PROTEIN S4, X ISOFORM 1 241 0.0000000
7 g13143.t26 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 1 241 0.0000000
13 g13143.t26 PIRSF PIRSF002116 RPS4a_RPS4e 1 223 0.0000000
1 g13143.t26 Pfam PF08071 RS4NT (NUC023) domain 1 21 0.0000001
3 g13143.t26 Pfam PF01479 S4 domain 25 72 0.0000000
5 g13143.t26 Pfam PF00900 Ribosomal family S4e 77 151 0.0000000
2 g13143.t26 Pfam PF00467 KOW motif 160 192 0.0000038
4 g13143.t26 Pfam PF16121 40S ribosomal protein S4 C-terminus 194 241 0.0000000
18 g13143.t26 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 24 87 10.7550000
16 g13143.t26 SMART SM00363 s4_6 24 88 0.0002200
17 g13143.t26 SMART SM00739 kow_9 156 183 0.0023000
9 g13143.t26 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 33 117 0.0000017

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. There were no conditions that were differentially expressed