Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S9.

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 g7115 g7115.t114 TTS g7115.t114 21263047 21263047
chr_2 g7115 g7115.t114 isoform g7115.t114 21263156 21264444
chr_2 g7115 g7115.t114 exon g7115.t114.exon1 21263156 21263271
chr_2 g7115 g7115.t114 exon g7115.t114.exon2 21263776 21263831
chr_2 g7115 g7115.t114 cds g7115.t114.CDS1 21263823 21263831
chr_2 g7115 g7115.t114 exon g7115.t114.exon3 21264054 21264444
chr_2 g7115 g7115.t114 cds g7115.t114.CDS2 21264054 21264437
chr_2 g7115 g7115.t114 TSS g7115.t114 21264887 21264887

Sequences

>g7115.t114 Gene=g7115 Length=563
TTTCATCATGGTTAATCACAGAATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAG
ACGTCCATATGAAAAACCTCGCTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCT
CCGTAACAAGCGTGAGGTATGGCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGC
TCGTGAATTGCTTACACTTGAAGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCT
TCTTCGTCGTCTTGTTCGTATTGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGT
TCTTGGTTTAAAAATTGAAGATTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACT
CGGTTTGGCTAAATCTTATCATCATGCTCGCCGTTCGTAAACAAGTCGTCAACATCCCAT
CATTTGTCGTTCGTTTGGACTCGCAGATTGATTTCTCATTGAAGTCACCATTCGGTGGTG
GACGACCAGGTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGGTGGCG
CTGATGAAGAAGAAGAGGATTAA

>g7115.t114 Gene=g7115 Length=130
MVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFGLRNKREVWRVKYTLAKIRKAARE
LLTLEEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL
AKSYHHARRS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g7115.t114 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 8 128 0
2 g7115.t114 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 8 128 0
4 g7115.t114 SMART SM01390 Ribosomal_S4_2 4 108 0
3 g7115.t114 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 12 129 0
5 g7115.t114 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 11 129 0

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:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0015935 small ribosomal subunit CC
GO:0019843 rRNA binding MF

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