Gene loci information

Transcript annotation

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

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.t6 TTS g11600.t6 17408974 17408974
chr_1 g11600 g11600.t6 isoform g11600.t6 17409067 17410315
chr_1 g11600 g11600.t6 exon g11600.t6.exon1 17409067 17409574
chr_1 g11600 g11600.t6 cds g11600.t6.CDS1 17409067 17409574
chr_1 g11600 g11600.t6 exon g11600.t6.exon2 17409631 17409827
chr_1 g11600 g11600.t6 cds g11600.t6.CDS2 17409631 17409827
chr_1 g11600 g11600.t6 exon g11600.t6.exon3 17410307 17410315
chr_1 g11600 g11600.t6 cds g11600.t6.CDS3 17410307 17410315
chr_1 g11600 g11600.t6 TSS g11600.t6 17410361 17410361

Sequences

>g11600.t6 Gene=g11600 Length=714
ATGAACACTTTTGTCGCCGCTGGCGTCTTTAAAGCTGAATTGAATGAGTTTTTAACTCGA
GAGCTCGCAGAGGATGGATATTCAGGAGTTGAAGTACGTGTGACACCATCAAGAACAGAA
ATCATTATTATGGCCACAAGAACTCAAAATGTTTTGGGTGAAAAAGGTCGTCGTATTCGT
GAATTAACAGCTGTTGTACAAAAGAGATTCAATTTTGCACCCGGTGCAGTTGAATTGTAT
GCTGAAAAAGTTGCTACCCGTGGTCTCTGCGCTATTGCACAAGCCGAGTCTCTTCGATAC
AAACTCATTGGTGGCTTAGCTGTTCGTCGTGCATGCTATGGTGTTCTTCGCTTCATTATG
GAATCAGGAGCTAAGGGCTGCGAAGTTGTTGTATCTGGCAAACTTAGAGGTCAACGTGCC
AAGTCAATGAAATTTGTTGATGGGTTGATGATTCATTCAGGTGATCCTTGCAATGACTAC
GTTGATACAGCCACACGTCATGTCTTATTGAGACAAGGAGTATTGGGAATTAAGGTCAAA
ATTATGCTACCATGGGATCCATCAGGCAAAATTGGTCCAAAACGACCATTGCCAGATAAC
GTTTCGGTTGTTGAACCTAAAGATGAGATCGTATATTTGAAACCTGACACCGAATACAAA
GGCAAACCAGCATATATTGGTGCTGAAGAACAGCAGCATGTCGAAGCTAAGTAA

>g11600.t6 Gene=g11600 Length=237
MNTFVAAGVFKAELNEFLTRELAEDGYSGVEVRVTPSRTEIIIMATRTQNVLGEKGRRIR
ELTAVVQKRFNFAPGAVELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRACYGVLRFIM
ESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVDTATRHVLLRQGVLGIKVK
IMLPWDPSGKIGPKRPLPDNVSVVEPKDEIVYLKPDTEYKGKPAYIGAEEQQHVEAK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11600.t6 CDD cd02413 40S_S3_KH 8 88 1.9873E-51
7 g11600.t6 Gene3D G3DSA:3.30.300.20 - 4 84 2.8E-42
8 g11600.t6 Gene3D G3DSA:3.30.1140.32 - 86 213 1.8E-70
3 g11600.t6 PANTHER PTHR11760:SF36 40S RIBOSOMAL PROTEIN S3 3 226 7.3E-133
4 g11600.t6 PANTHER PTHR11760 30S/40S RIBOSOMAL PROTEIN S3 3 226 7.3E-133
1 g11600.t6 Pfam PF07650 KH domain 13 86 2.7E-11
2 g11600.t6 Pfam PF00189 Ribosomal protein S3, C-terminal domain 99 181 5.8E-23
10 g11600.t6 ProSitePatterns PS00548 Ribosomal protein S3 signature. 140 176 -
11 g11600.t6 ProSiteProfiles PS50823 Type-2 KH domain profile. 14 85 11.916
5 g11600.t6 SUPERFAMILY SSF54814 Prokaryotic type KH domain (KH-domain type II) 4 92 9.16E-25
6 g11600.t6 SUPERFAMILY SSF54821 Ribosomal protein S3 C-terminal domain 87 185 4.32E-28
12 g11600.t6 TIGRFAM TIGR01008 uS3_euk_arch: ribosomal protein uS3 3 204 4.8E-71

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

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