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.t175 TTS g7115.t175 21263047 21263047
chr_2 g7115 g7115.t175 isoform g7115.t175 21263156 21264887
chr_2 g7115 g7115.t175 exon g7115.t175.exon1 21263156 21263270
chr_2 g7115 g7115.t175 exon g7115.t175.exon2 21263970 21264446
chr_2 g7115 g7115.t175 cds g7115.t175.CDS1 21264024 21264437
chr_2 g7115 g7115.t175 exon g7115.t175.exon3 21264852 21264887
chr_2 g7115 g7115.t175 TSS g7115.t175 21264887 21264887

Sequences

>g7115.t175 Gene=g7115 Length=628
CTTTTCGAAAAATTCTTGCAAAAAGAATTTTGTCAAGTTTTCATCATGGTTAATCACAGA
ATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAGACGTCCATATGAAAAACCTCGC
TTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCTCCGTAACAAGCGTGAGGTATGG
CGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGCTCGTGAATTGCTTACACTTGAA
GAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCTTCTTCGTCGTCTTGTTCGTATT
GGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGTTCTTGGTTTAAAAATTGAAGAT
TTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACTCGGTTTGGCTAAATCTTATCAT
CATGCTCGCGTTCTTATCCGACAAAGACATATTCGGTAAGTTAAATTACAAACCAAACAG
TAATGAAATGTTTCTTTTTAAAATGATGAAGACTGATTTCTCATTGAAGTCACCATTCGG
TGGTGGACGACCAGGTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGG
TGGCGCTGATGAAGAAGAAGAGGATTAA

>g7115.t175 Gene=g7115 Length=137
MVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFGLRNKREVWRVKYTLAKIRKAARE
LLTLEEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL
AKSYHHARVLIRQRHIR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g7115.t175 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 8 137 1.3E-64
2 g7115.t175 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 8 137 1.3E-64
5 g7115.t175 ProSitePatterns PS00632 Ribosomal protein S4 signature. 107 131 -
4 g7115.t175 SMART SM01390 Ribosomal_S4_2 4 108 2.3E-17
3 g7115.t175 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 12 137 1.57E-26
6 g7115.t175 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 11 137 7.8E-53

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