Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t83 TSS g13143.t83 28150713 28150713
chr_1 g13143 g13143.t83 isoform g13143.t83 28150731 28152591
chr_1 g13143 g13143.t83 exon g13143.t83.exon1 28150731 28150739
chr_1 g13143 g13143.t83 exon g13143.t83.exon2 28151200 28151467
chr_1 g13143 g13143.t83 cds g13143.t83.CDS1 28151260 28151467
chr_1 g13143 g13143.t83 exon g13143.t83.exon3 28151695 28151796
chr_1 g13143 g13143.t83 cds g13143.t83.CDS2 28151695 28151796
chr_1 g13143 g13143.t83 exon g13143.t83.exon4 28152163 28152591
chr_1 g13143 g13143.t83 cds g13143.t83.CDS3 28152163 28152203
chr_1 g13143 g13143.t83 TTS g13143.t83 28152716 28152716

Sequences

>g13143.t83 Gene=g13143 Length=808
CCTAAGTAATGATTGTAGGCTCGCGGTCCGAAAAAACATTTGAAGCGTTTAGCAGCTCCA
AAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCATCAACCGGTCCT
CATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGCTTGAAGTATGCT
TTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCAAAGTTGATGGAAAA
GTCAGAACAGATATCAATTATCCAGCAGGTTTCATGGATGTCATCACCATTGAGAAAACT
GGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACAATCCATCGCATTACT
GCCGATGAAGCAAAAGTAATACAAGTTATGCAAAGTGAAGCGTGTAACAATTGGACCTAA
GAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCCAGATCCAAACAT
TCATGTAAACGACACAATTCAATTAGATATTGCAACTGGAAAAATCACAGATCATATTCG
TTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGGTCGAGTTGGTAC
TGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGTGAAAGACGCTAA
TGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAAAGGCGCAAAGGC
ATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGAAGAACGCGATAA
GCGATTGGCACAAAAAACCACTAACTAA

>g13143.t83 Gene=g13143 Length=116
MLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTETKKIVMQRHIKVDGKVRT
DINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAKVIQVMQSEACNNWT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13143.t83 CDD cd00165 S4 26 94 0.0000001
8 g13143.t83 Gene3D G3DSA:3.10.290.40 - 1 99 0.0000000
4 g13143.t83 PANTHER PTHR11581:SF33 40S RIBOSOMAL PROTEIN S4 1 102 0.0000000
5 g13143.t83 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 1 102 0.0000000
1 g13143.t83 Pfam PF08071 RS4NT (NUC023) domain 1 21 0.0000000
2 g13143.t83 Pfam PF01479 S4 domain 25 72 0.0000000
3 g13143.t83 Pfam PF00900 Ribosomal family S4e 77 103 0.0000000
9 g13143.t83 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 24 87 10.7550000
7 g13143.t83 SMART SM00363 s4_6 24 88 0.0002200
6 g13143.t83 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 33 87 0.0000007

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. There were no conditions that were differentially expressed