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.t13 TSS g13143.t13 28150713 28150713
chr_1 g13143 g13143.t13 isoform g13143.t13 28150723 28152591
chr_1 g13143 g13143.t13 exon g13143.t13.exon1 28150723 28150735
chr_1 g13143 g13143.t13 exon g13143.t13.exon2 28151192 28151467
chr_1 g13143 g13143.t13 cds g13143.t13.CDS1 28151260 28151467
chr_1 g13143 g13143.t13 exon g13143.t13.exon3 28151695 28151796
chr_1 g13143 g13143.t13 cds g13143.t13.CDS2 28151695 28151796
chr_1 g13143 g13143.t13 exon g13143.t13.exon4 28152163 28152591
chr_1 g13143 g13143.t13 cds g13143.t13.CDS3 28152163 28152203
chr_1 g13143 g13143.t13 TTS g13143.t13 28152716 28152716

Sequences

>g13143.t13 Gene=g13143 Length=820
TTGTCAATCCTAAATTTCTTGTGATTGTAGGCTCGCGGTCCGAAAAAACATTTGAAGCGT
TTAGCAGCTCCAAAAGCATGGATGCTGGACAAATTAGGAGGTCCGTTCGCTCCTCGTCCA
TCAACCGGTCCTCATAAATTGCGTGAATCACTTCCTTTGGTCATTTTCTTGCGCAATCGC
TTGAAGTATGCTTTGACCAACACTGAAACTAAGAAAATTGTCATGCAAAGACACATCAAA
GTTGATGGAAAAGTCAGAACAGATATCAATTATCCAGCAGGTTTCATGGATGTCATCACC
ATTGAGAAAACTGGTGAATTCTTCCGTTTGATCTATGATGTAAAGGGTCGTTTTACAATC
CATCGCATTACTGCCGATGAAGCAAAAGTAATACAAGTTATGCAAAGTGAAGCGTGTAAC
AATTGGACCTAAGAAGATTCCATACTTGGTCACACATGATGGTCGTACACTCCGTTATCC
AGATCCAAACATTCATGTAAACGACACAATTCAATTAGATATTGCAACTGGAAAAATCAC
AGATCATATTCGTTTTGAATCCGGCAATTTGGTTATGGTTACTGGAGGTCGTAACTTGGG
TCGAGTTGGTACTGTTGTGAATCGTGAAAAGCATCCTGGTTCATTTGAAATCATTCATGT
GAAAGACGCTAATGGACATATGTTTGCTACTCGTTTGACAAACATTTTCATCATCGGAAA
AGGCGCAAAGGCATACATTTCATTGCCTAAAGGCAAGGGTATTAAACTCAGTGTTGCCGA
AGAACGCGATAAGCGATTGGCACAAAAAACCACTAACTAA

>g13143.t13 Gene=g13143 Length=116
MLDKLGGPFAPRPSTGPHKLRESLPLVIFLRNRLKYALTNTETKKIVMQRHIKVDGKVRT
DINYPAGFMDVITIEKTGEFFRLIYDVKGRFTIHRITADEAKVIQVMQSEACNNWT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g13143.t13 CDD cd00165 S4 26 94 0.0000001
8 g13143.t13 Gene3D G3DSA:3.10.290.40 - 1 99 0.0000000
4 g13143.t13 PANTHER PTHR11581:SF33 40S RIBOSOMAL PROTEIN S4 1 102 0.0000000
5 g13143.t13 PANTHER PTHR11581 30S/40S RIBOSOMAL PROTEIN S4 1 102 0.0000000
1 g13143.t13 Pfam PF08071 RS4NT (NUC023) domain 1 21 0.0000000
2 g13143.t13 Pfam PF01479 S4 domain 25 72 0.0000000
3 g13143.t13 Pfam PF00900 Ribosomal family S4e 77 103 0.0000000
9 g13143.t13 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 24 87 10.7550000
7 g13143.t13 SMART SM00363 s4_6 24 88 0.0002200
6 g13143.t13 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