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.t20 TSS g13143.t20 28150713 28150713
chr_1 g13143 g13143.t20 isoform g13143.t20 28150723 28152591
chr_1 g13143 g13143.t20 exon g13143.t20.exon1 28150723 28150735
chr_1 g13143 g13143.t20 exon g13143.t20.exon2 28151120 28151139
chr_1 g13143 g13143.t20 cds g13143.t20.CDS1 28151137 28151139
chr_1 g13143 g13143.t20 exon g13143.t20.exon3 28151209 28151458
chr_1 g13143 g13143.t20 cds g13143.t20.CDS2 28151209 28151458
chr_1 g13143 g13143.t20 exon g13143.t20.exon4 28151695 28151792
chr_1 g13143 g13143.t20 cds g13143.t20.CDS3 28151695 28151792
chr_1 g13143 g13143.t20 exon g13143.t20.exon5 28152163 28152591
chr_1 g13143 g13143.t20 cds g13143.t20.CDS4 28152163 28152591
chr_1 g13143 g13143.t20 TTS g13143.t20 28152716 28152716

Sequences

>g13143.t20 Gene=g13143 Length=810
TTGTCAATCCTAAGTAATTAACTTTGGGAAATGGCTCGCGGTCCGAAAAAACATTTGAAG
CGTTTAGCAGCTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGT
CCATCAACCGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAAT
CGCTTGAAGTATGCTTTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATC
AAAGTTGATGGAAAAGTCAGAACAGATATCAATTATCCAGCAGATGTCATCACCATTGAG
AAAACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACAATCCATCGC
ATTACTGCCGATGAAGCAAAATACAAGTTATGCAAAGTGAAGCGTGTAACAATTGGACCT
AAGAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCCAGATCCAAAC
ATTCATGTAAACGACACAATTCAATTAGATATTGCAACTGGAAAAATCACAGATCATATT
CGTTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGGTCGAGTTGGT
ACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTGAAAGACGCT
AATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAAGGCGCAAAG
GCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAAGAACGCGAT
AAGCGATTGGCACAAAAAACCACTAACTAA

>g13143.t20 Gene=g13143 Length=259
MARGPKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTE
TKKIVMQRHIKVDGKVRTDINYPADVITIEKTGEFFRLIYDVKGRFTIHRITADEAKYKL
CKVKRVTIGPKKIPYLVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFESGNLVMV
TGGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMFATRLTNIFIIGKGAKAYISLPKGKG
IKLSVAEERDKRLAQKTTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g13143.t20 CDD cd00165 S4 44 109 5.52156E-5
14 g13143.t20 CDD cd06087 KOW_RPS4 172 226 1.16727E-28
10 g13143.t20 Gene3D G3DSA:3.10.290.40 - 1 114 3.4E-55
12 g13143.t20 Gene3D G3DSA:2.40.50.740 - 119 169 6.4E-29
11 g13143.t20 Gene3D G3DSA:2.30.30.30 - 172 242 4.1E-36
8 g13143.t20 Hamap MF_00485 30S ribosomal protein S4e [rps4e]. 7 235 33.820774
6 g13143.t20 PANTHER PTHR11581:SF30 40S RIBOSOMAL PROTEIN S4, X ISOFORM 1 256 9.9E-133
7 g13143.t20 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 1 256 9.9E-133
13 g13143.t20 PIRSF PIRSF002116 RPS4a_RPS4e 1 238 6.4E-94
1 g13143.t20 Pfam PF08071 RS4NT (NUC023) domain 3 39 8.0E-20
3 g13143.t20 Pfam PF01479 S4 domain 43 84 1.9E-7
5 g13143.t20 Pfam PF00900 Ribosomal family S4e 92 166 3.2E-36
2 g13143.t20 Pfam PF00467 KOW motif 175 207 4.1E-6
4 g13143.t20 Pfam PF16121 40S ribosomal protein S4 C-terminus 209 256 6.2E-26
17 g13143.t20 ProSitePatterns PS00528 Ribosomal protein S4e signature. 8 22 -
18 g13143.t20 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 42 102 8.868
16 g13143.t20 SMART SM00739 kow_9 171 198 0.0023
9 g13143.t20 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 51 131 4.58E-5

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