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.t94 TSS g13143.t94 28151119 28151119
chr_1 g13143 g13143.t94 isoform g13143.t94 28151137 28152591
chr_1 g13143 g13143.t94 exon g13143.t94.exon1 28151137 28151139
chr_1 g13143 g13143.t94 cds g13143.t94.CDS1 28151137 28151139
chr_1 g13143 g13143.t94 exon g13143.t94.exon2 28151221 28151467
chr_1 g13143 g13143.t94 cds g13143.t94.CDS2 28151221 28151467
chr_1 g13143 g13143.t94 exon g13143.t94.exon3 28151695 28151792
chr_1 g13143 g13143.t94 cds g13143.t94.CDS3 28151695 28151792
chr_1 g13143 g13143.t94 exon g13143.t94.exon4 28152163 28152591
chr_1 g13143 g13143.t94 cds g13143.t94.CDS4 28152163 28152591
chr_1 g13143 g13143.t94 TTS g13143.t94 28152716 28152716

Sequences

>g13143.t94 Gene=g13143 Length=777
ATGAAAAAACATTTGAAGCGTTTAGCAGCTCCAAAAGCATGGATGCTGGACAAATTAGGA
GGTCCGTTCGCTCCTCGTCCATCAACCGGTCCTCATAAATTGCGTGAATCACTTCCTTTG
GTCATTTTCTTGCGCAATCGCTTGAAGTATGCTTTGACCAACACTGAAACTAAGAAAATT
GTCATGCAAAGACACATCAAAGTTGATGGAAAAGTCAGAACAGATATCAATTATCCAGCA
GGTTTCATGGATGTCATCACCATTGAGAAAACTGGTGAATTCTTCCGTTTGATCTATGAT
GTAAAGGGTCGTTTTACAATCCATCGCATTACTGCCGATGAAGCAAAATACAAGTTATGC
AAAGTGAAGCGTGTAACAATTGGACCTAAGAAGATTCCATACTTGGTCACACATGATGGT
CGTACACTCCGTTATCCAGATCCAAACATTCATGTAAACGACACAATTCAATTAGATATT
GCAACTGGAAAAATCACAGATCATATTCGTTTTGAATCCGGCAATTTGGTTATGGTTACT
GGAGGTCGTAACTTGGGTCGAGTTGGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCA
TTTGAAATCATTCATGTGAAAGACGCTAATGGACATATGTTTGCTACTCGTTTGACAAAC
ATTTTCATCATCGGAAAAGGCGCAAAGGCATACATTTCATTGCCTAAAGGCAAGGGTATT
AAACTCAGTGTTGCCGAAGAACGCGATAAGCGATTGGCACAAAAAACCACTAACTAA

>g13143.t94 Gene=g13143 Length=258
MKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTETKKI
VMQRHIKVDGKVRTDINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAKYKLC
KVKRVTIGPKKIPYLVTHDGRTLRYPDPNIHVNDTIQLDIATGKITDHIRFESGNLVMVT
GGRNLGRVGTVVNREKHPGSFEIIHVKDANGHMFATRLTNIFIIGKGAKAYISLPKGKGI
KLSVAEERDKRLAQKTTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g13143.t94 CDD cd00165 S4 40 108 2.50099E-6
14 g13143.t94 CDD cd06087 KOW_RPS4 171 225 1.78653E-28
10 g13143.t94 Gene3D G3DSA:3.10.290.40 - 1 113 5.5E-58
12 g13143.t94 Gene3D G3DSA:2.40.50.740 - 118 168 6.3E-29
11 g13143.t94 Gene3D G3DSA:2.30.30.30 - 171 241 4.1E-36
8 g13143.t94 Hamap MF_00485 30S ribosomal protein S4e [rps4e]. 3 234 36.502556
6 g13143.t94 PANTHER PTHR11581:SF30 40S RIBOSOMAL PROTEIN S4, X ISOFORM 2 255 1.9E-134
7 g13143.t94 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 2 255 1.9E-134
13 g13143.t94 PIRSF PIRSF002116 RPS4a_RPS4e 1 237 1.5E-98
1 g13143.t94 Pfam PF08071 RS4NT (NUC023) domain 2 35 2.7E-18
3 g13143.t94 Pfam PF01479 S4 domain 39 86 1.4E-9
5 g13143.t94 Pfam PF00900 Ribosomal family S4e 91 165 3.2E-36
2 g13143.t94 Pfam PF00467 KOW motif 174 206 4.1E-6
4 g13143.t94 Pfam PF16121 40S ribosomal protein S4 C-terminus 208 255 6.1E-26
18 g13143.t94 ProSitePatterns PS00528 Ribosomal protein S4e signature. 4 18 -
19 g13143.t94 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 38 101 10.755
16 g13143.t94 SMART SM00363 s4_6 38 102 2.2E-4
17 g13143.t94 SMART SM00739 kow_9 170 197 0.0023
9 g13143.t94 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 47 130 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