Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t25 isoform g7115.t25 21263043 21264423
chr_2 g7115 g7115.t25 exon g7115.t25.exon1 21263043 21263275
chr_2 g7115 g7115.t25 TTS g7115.t25 21263047 21263047
chr_2 g7115 g7115.t25 exon g7115.t25.exon2 21263994 21264423
chr_2 g7115 g7115.t25 cds g7115.t25.CDS1 21264024 21264161
chr_2 g7115 g7115.t25 TSS g7115.t25 21264887 21264887

Sequences

>g7115.t25 Gene=g7115 Length=663
AATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAGACGTCCATATGAAAAACCTCG
CTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCTCCGTAACAAGCGTGAGGTATG
GCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGCTCGTGAATTGCTTACACTTGA
AGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCTTCTTCGTCGTCTTGTTCGTAT
TGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGTTCTTGGTTTAAAAATTGAAGA
TTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACTCGGTTTGGCTAAATCTTATCA
TCATGCTCGCGTTCTTATCCGACAAAGACATATTCGGTAAGTTAAATTACAAACCAAACA
GTAATGAAATNNCATTGATTTCTCATTGAAGTCACCATTCGGTGGTGGACGACCAGGTCG
CGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGGTGGCGCTGATGAAGAAGA
AGAGGATTAAACTGGAATTCACAGCAACATCTTTTCGCAACAAAAAATCTTATTAAAATC
TTTTCCAGTTGGTGTGTGCGATAAAAAAGAACATTCAAACATAATAAATGAAAATTGATA
AAA

>g7115.t25 Gene=g7115 Length=45
MKLDYVLGLKIEDFLERRLQTQVFKLGLAKSYHHARVLIRQRHIR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t25 Gene3D G3DSA:3.10.290.10 - 16 45 1.0E-5
2 g7115.t25 PANTHER PTHR11831:SF5 40S RIBOSOMAL PROTEIN S9 1 45 1.8E-23
3 g7115.t25 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 1 45 1.8E-23
1 g7115.t25 Pfam PF01479 S4 domain 17 45 1.3E-5
5 g7115.t25 ProSitePatterns PS00632 Ribosomal protein S4 signature. 15 39 -
4 g7115.t25 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 2 45 4.56E-12

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:0003723 RNA binding MF
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