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.t19 TTS g9066.t19 35013961 35013961
chr_2 g9066 g9066.t19 isoform g9066.t19 35014027 35015255
chr_2 g9066 g9066.t19 exon g9066.t19.exon1 35014027 35014095
chr_2 g9066 g9066.t19 cds g9066.t19.CDS1 35014027 35014095
chr_2 g9066 g9066.t19 exon g9066.t19.exon2 35014276 35014474
chr_2 g9066 g9066.t19 cds g9066.t19.CDS2 35014276 35014474
chr_2 g9066 g9066.t19 exon g9066.t19.exon3 35014695 35014854
chr_2 g9066 g9066.t19 cds g9066.t19.CDS3 35014695 35014854
chr_2 g9066 g9066.t19 exon g9066.t19.exon4 35015248 35015255
chr_2 g9066 g9066.t19 cds g9066.t19.CDS4 35015248 35015254
chr_2 g9066 g9066.t19 TSS g9066.t19 35015280 35015280

Sequences

>g9066.t19 Gene=g9066 Length=436
ATGGGTGCGAAAACCAAGAGGAATTCGAACTGCTCGTAAGCTTAAAACACACAGACGTGA
CCAACGATGGGCTGACAAAGATTATAAGAAAGCTCACTTGGGTACTCGCTGGAAGGCAAA
TCCATTTGGAGGTGCATCTCATGCTAAGGGAATCGTTCTTGAAAAAGTTGGTGTTGAAGC
TAAACAGCCAAACTCAGCTATCCGCAAGTGCGTTCGTGTACAATTGATCAAGAATGGCAA
GAAAATTACCGCTTTCGTTCCTCGTGATGGTTGCTTAAACTATATTGAAGAAAATGACGA
AGTTTTGGTTGCAGGTTTTGGTCGTAAAGGTCACGCTGTTGGTGATATTCCCGGAGTAAG
ATTTAAGGTCGTCAAAGTAGCAAATGTTTCGCTATTGGCCTTATACAAGGAAAAGAAAGA
GCGACCACGTTCATAA

>g9066.t19 Gene=g9066 Length=144
WVRKPRGIRTARKLKTHRRDQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEA
KQPNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGDIPGVR
FKVVKVANVSLLALYKEKKERPRS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9066.t19 CDD cd03367 Ribosomal_S23 27 141 4.91103E-81
5 g9066.t19 Gene3D G3DSA:2.40.50.140 - 26 144 3.8E-69
9 g9066.t19 MobiDBLite mobidb-lite consensus disorder prediction 1 21 -
10 g9066.t19 MobiDBLite mobidb-lite consensus disorder prediction 1 17 -
2 g9066.t19 PANTHER PTHR11652:SF14 40S RIBOSOMAL PROTEIN S23 3 144 1.3E-84
3 g9066.t19 PANTHER PTHR11652 30S RIBOSOMAL PROTEIN S12 FAMILY MEMBER 3 144 1.3E-84
6 g9066.t19 PIRSF PIRSF002133 RPS12p_RPS12a_RPS23e_RPS12o 17 144 2.6E-35
1 g9066.t19 Pfam PF00164 Ribosomal protein S12/S23 31 143 5.2E-52
8 g9066.t19 ProSitePatterns PS00055 Ribosomal protein S12 signature. 61 68 -
4 g9066.t19 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 21 142 1.8E-36
11 g9066.t19 TIGRFAM TIGR00982 uS12_E_A: ribosomal protein uS12 8 143 1.2E-56

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