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.t9 TTS g9066.t9 35013961 35013961
chr_2 g9066 g9066.t9 isoform g9066.t9 35014027 35014855
chr_2 g9066 g9066.t9 exon g9066.t9.exon1 35014027 35014095
chr_2 g9066 g9066.t9 cds g9066.t9.CDS1 35014028 35014095
chr_2 g9066 g9066.t9 exon g9066.t9.exon2 35014302 35014474
chr_2 g9066 g9066.t9 cds g9066.t9.CDS2 35014302 35014474
chr_2 g9066 g9066.t9 exon g9066.t9.exon3 35014695 35014855
chr_2 g9066 g9066.t9 cds g9066.t9.CDS3 35014695 35014855
chr_2 g9066 g9066.t9 TSS g9066.t9 35015280 35015280

Sequences

>g9066.t9 Gene=g9066 Length=403
GGAAAACCAAGAGGAATTCGAACTGCTCGTAAGCTTAAAACACACAGACGTGACCAACGA
TGGGCTGACAAAGATTATAAGAAAGCTCACTTGGGTACTCGCTGGAAGGCAAATCCATTT
GGAGGTGCATCTCATGCTAAGGGAATCGTTCTTGAAAAAGTTGGTGTTGAAGCTAAACAG
CCAAACTCAGCTATCCGCAAGTGCGTTCGTGTACAATTGATCAAGAATGGCAAGAAAATT
ACCGCTTTCGTTCCTCGTGATGGTTGCTTAAACTATATTGAAGAAAATGACGAAGTTTTG
GTTGCAGGTTTTGGTCGTAAAGGTCACGCTGTTGGTCGTCAAAGTAGCAAATGTTTCGCT
ATTGGCCTTATACAAGGAAAAGAAAGAGCGACCACGTTCATAA

>g9066.t9 Gene=g9066 Length=134
GKPRGIRTARKLKTHRRDQRWADKDYKKAHLGTRWKANPFGGASHAKGIVLEKVGVEAKQ
PNSAIRKCVRVQLIKNGKKITAFVPRDGCLNYIEENDEVLVAGFGRKGHAVGRQSSKCFA
IGLIQGKERATTFI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g9066.t9 Gene3D G3DSA:2.40.50.140 - 24 126 1.5E-50
6 g9066.t9 MobiDBLite mobidb-lite consensus disorder prediction 1 25 -
7 g9066.t9 MobiDBLite mobidb-lite consensus disorder prediction 1 15 -
2 g9066.t9 PANTHER PTHR11652:SF14 40S RIBOSOMAL PROTEIN S23 1 123 1.4E-67
3 g9066.t9 PANTHER PTHR11652 30S RIBOSOMAL PROTEIN S12 FAMILY MEMBER 1 123 1.4E-67
1 g9066.t9 Pfam PF00164 Ribosomal protein S12/S23 29 114 5.8E-38
5 g9066.t9 ProSitePatterns PS00055 Ribosomal protein S12 signature. 59 66 -
4 g9066.t9 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 19 107 1.29E-27
9 g9066.t9 TIGRFAM TIGR00982 uS12_E_A: ribosomal protein uS12 6 113 5.9E-43

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

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