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.t78 TSS g13143.t78 28150713 28150713
chr_1 g13143 g13143.t78 isoform g13143.t78 28150731 28152591
chr_1 g13143 g13143.t78 exon g13143.t78.exon1 28150731 28150735
chr_1 g13143 g13143.t78 exon g13143.t78.exon2 28151120 28151139
chr_1 g13143 g13143.t78 cds g13143.t78.CDS1 28151137 28151139
chr_1 g13143 g13143.t78 exon g13143.t78.exon3 28151209 28151467
chr_1 g13143 g13143.t78 cds g13143.t78.CDS2 28151209 28151467
chr_1 g13143 g13143.t78 exon g13143.t78.exon4 28151695 28151796
chr_1 g13143 g13143.t78 cds g13143.t78.CDS3 28151695 28151796
chr_1 g13143 g13143.t78 exon g13143.t78.exon5 28152163 28152591
chr_1 g13143 g13143.t78 cds g13143.t78.CDS4 28152163 28152203
chr_1 g13143 g13143.t78 TTS g13143.t78 28152716 28152716

Sequences

>g13143.t78 Gene=g13143 Length=815
CCTAAGTAATTAACTTTGGGAAATGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGC
AGCTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAAC
CGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAA
GTATGCTTTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGA
TGGAAAAGTCAGAACAGATATCAATTATCCAGCAGGTTTCATGGATGTCATCACCATTGA
GAAAACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACAATCCATCG
CATTACTGCCGATGAAGCAAAAGTAATACAAGTTATGCAAAGTGAAGCGTGTAACAATTG
GACCTAAGAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCCAGATC
CAAACATTCATGTAAACGACACAATTCAATTAGATATTGCAACTGGAAAAATCACAGATC
ATATTCGTTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGGTCGAG
TTGGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTGAAAG
ACGCTAATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAAGGCG
CAAAGGCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAAGAAC
GCGATAAGCGATTGGCACAAAAAACCACTAACTAA

>g13143.t78 Gene=g13143 Length=134
MARGPKKHLKRLAAPKAWMLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTE
TKKIVMQRHIKVDGKVRTDINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAK
VIQVMQSEACNNWT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13143.t78 CDD cd00165 S4 44 112 1.41847E-7
7 g13143.t78 Gene3D G3DSA:3.10.290.40 - 1 117 1.3E-61
4 g13143.t78 PANTHER PTHR11581:SF33 40S RIBOSOMAL PROTEIN S4 2 120 1.6E-68
5 g13143.t78 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 2 120 1.6E-68
1 g13143.t78 Pfam PF08071 RS4NT (NUC023) domain 3 39 2.7E-20
2 g13143.t78 Pfam PF01479 S4 domain 43 90 4.2E-10
3 g13143.t78 Pfam PF00900 Ribosomal family S4e 95 121 3.5E-8
9 g13143.t78 ProSitePatterns PS00528 Ribosomal protein S4e signature. 8 22 -
11 g13143.t78 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 42 105 10.755
10 g13143.t78 SMART SM00363 s4_6 42 106 2.2E-4
6 g13143.t78 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 47 109 9.68E-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