Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S3-B.

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 g11600 g11600.t9 TTS g11600.t9 17408974 17408974
chr_1 g11600 g11600.t9 isoform g11600.t9 17409067 17410315
chr_1 g11600 g11600.t9 exon g11600.t9.exon1 17409067 17409574
chr_1 g11600 g11600.t9 cds g11600.t9.CDS1 17409067 17409574
chr_1 g11600 g11600.t9 exon g11600.t9.exon2 17409631 17409696
chr_1 g11600 g11600.t9 cds g11600.t9.CDS2 17409631 17409696
chr_1 g11600 g11600.t9 exon g11600.t9.exon3 17410248 17410315
chr_1 g11600 g11600.t9 cds g11600.t9.CDS3 17410248 17410252
chr_1 g11600 g11600.t9 TSS g11600.t9 17410361 17410361

Sequences

>g11600.t9 Gene=g11600 Length=642
ATGAACACTGCAATTTCAAAAAAACGCAAGGTAGATGACAATAATTAACAAACAATTTAT
TGAATGAGAACTCAAAATGTTTTGGGTGAAAAAGGTCGTCGTATTCGTGAATTAACAGCT
GTTGTACAAAAGAGATTCAATTTTGCACCCGGTGCAGTTGAATTGTATGCTGAAAAAGTT
GCTACCCGTGGTCTCTGCGCTATTGCACAAGCCGAGTCTCTTCGATACAAACTCATTGGT
GGCTTAGCTGTTCGTCGTGCATGCTATGGTGTTCTTCGCTTCATTATGGAATCAGGAGCT
AAGGGCTGCGAAGTTGTTGTATCTGGCAAACTTAGAGGTCAACGTGCCAAGTCAATGAAA
TTTGTTGATGGGTTGATGATTCATTCAGGTGATCCTTGCAATGACTACGTTGATACAGCC
ACACGTCATGTCTTATTGAGACAAGGAGTATTGGGAATTAAGGTCAAAATTATGCTACCA
TGGGATCCATCAGGCAAAATTGGTCCAAAACGACCATTGCCAGATAACGTTTCGGTTGTT
GAACCTAAAGATGAGATCGTATATTTGAAACCTGACACCGAATACAAAGGCAAACCAGCA
TATATTGGTGCTGAAGAACAGCAGCATGTCGAAGCTAAGTAA

>g11600.t9 Gene=g11600 Length=192
MRTQNVLGEKGRRIRELTAVVQKRFNFAPGAVELYAEKVATRGLCAIAQAESLRYKLIGG
LAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTAT
RHVLLRQGVLGIKVKIMLPWDPSGKIGPKRPLPDNVSVVEPKDEIVYLKPDTEYKGKPAY
IGAEEQQHVEAK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11600.t9 Gene3D G3DSA:3.30.300.20 - 1 39 3.5E-15
8 g11600.t9 Gene3D G3DSA:3.30.1140.32 - 41 168 9.7E-71
2 g11600.t9 PANTHER PTHR11760:SF36 40S RIBOSOMAL PROTEIN S3 2 181 1.2E-103
3 g11600.t9 PANTHER PTHR11760 30S/40S RIBOSOMAL PROTEIN S3 2 181 1.2E-103
1 g11600.t9 Pfam PF00189 Ribosomal protein S3, C-terminal domain 54 136 3.6E-23
6 g11600.t9 ProSitePatterns PS00548 Ribosomal protein S3 signature. 95 131 -
4 g11600.t9 SUPERFAMILY SSF54814 Prokaryotic type KH domain (KH-domain type II) 2 47 5.67E-9
5 g11600.t9 SUPERFAMILY SSF54821 Ribosomal protein S3 C-terminal domain 42 140 2.62E-28
9 g11600.t9 TIGRFAM TIGR01008 uS3_euk_arch: ribosomal protein uS3 2 159 1.9E-51

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:0003723 RNA binding MF
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0015935 small ribosomal subunit CC

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