Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S23.

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_2 g9066 g9066.t18 TTS g9066.t18 35013961 35013961
chr_2 g9066 g9066.t18 isoform g9066.t18 35014027 35015255
chr_2 g9066 g9066.t18 exon g9066.t18.exon1 35014027 35014095
chr_2 g9066 g9066.t18 cds g9066.t18.CDS1 35014027 35014095
chr_2 g9066 g9066.t18 exon g9066.t18.exon2 35014288 35014474
chr_2 g9066 g9066.t18 cds g9066.t18.CDS2 35014288 35014474
chr_2 g9066 g9066.t18 exon g9066.t18.exon3 35014695 35014854
chr_2 g9066 g9066.t18 cds g9066.t18.CDS3 35014695 35014854
chr_2 g9066 g9066.t18 exon g9066.t18.exon4 35015252 35015255
chr_2 g9066 g9066.t18 cds g9066.t18.CDS4 35015252 35015255
chr_2 g9066 g9066.t18 TSS g9066.t18 35015280 35015280

Sequences

>g9066.t18 Gene=g9066 Length=420
ATGGGAAAACCAAGAGGAATTCGAACTGCTCGTAAGCTTAAAACACACAGACGTGACCAA
CGATGGGCTGACAAAGATTATAAGAAAGCTCACTTGGGTACTCGCTGGAAGGCAAATCCA
TTTGGAGGTGCATCTCATGCTAAGGGAATCGTTCTTGAAAAAGTTGGTGTTGAAGCTAAA
CAGCCAAACTCAGCTATCCGCAAGTGCGTTCGTGTACAATTGATCAAGAATGGCAAGAAA
ATTACCGCTTTCGTTCCTCGTGATGGTTGCTTAAACTATATTGAAGAAAATGACGAAGTT
TTGGTTGCAGGTTTTGGTCGTAAAGGTCACGCTGTTGGTGATATTCCCGGAGTCGTCAAA
GTAGCAAATGTTTCGCTATTGGCCTTATACAAGGAAAAGAAAGAGCGACCACGTTCATAA

>g9066.t18 Gene=g9066 Length=139
MGKPRGIRTARKLKTHRRDQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAK
QPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVVK
VANVSLLALYKEKKERPRS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9066.t18 CDD cd03367 Ribosomal_S23 26 136 1.68477E-75
5 g9066.t18 Gene3D G3DSA:2.40.50.140 - 25 139 1.1E-62
9 g9066.t18 MobiDBLite mobidb-lite consensus disorder prediction 1 16 -
10 g9066.t18 MobiDBLite mobidb-lite consensus disorder prediction 1 26 -
2 g9066.t18 PANTHER PTHR11652:SF14 40S RIBOSOMAL PROTEIN S23 1 139 1.5E-79
3 g9066.t18 PANTHER PTHR11652 30S RIBOSOMAL PROTEIN S12 FAMILY MEMBER 1 139 1.5E-79
6 g9066.t18 PIRSF PIRSF002133 RPS12p_RPS12a_RPS23e_RPS12o 16 139 4.2E-30
1 g9066.t18 Pfam PF00164 Ribosomal protein S12/S23 30 138 7.4E-46
8 g9066.t18 ProSitePatterns PS00055 Ribosomal protein S12 signature. 60 67 -
4 g9066.t18 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 20 137 8.57E-32
11 g9066.t18 TIGRFAM TIGR00982 uS12_E_A: ribosomal protein uS12 7 138 5.5E-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:0005840 ribosome CC
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