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.t124 TTS g7115.t124 21263047 21263047
chr_2 g7115 g7115.t124 isoform g7115.t124 21263156 21264446
chr_2 g7115 g7115.t124 exon g7115.t124.exon1 21263156 21263273
chr_2 g7115 g7115.t124 cds g7115.t124.CDS1 21263156 21263273
chr_2 g7115 g7115.t124 exon g7115.t124.exon2 21263772 21263817
chr_2 g7115 g7115.t124 cds g7115.t124.CDS2 21263772 21263817
chr_2 g7115 g7115.t124 exon g7115.t124.exon3 21264182 21264446
chr_2 g7115 g7115.t124 cds g7115.t124.CDS3 21264182 21264437
chr_2 g7115 g7115.t124 TSS g7115.t124 21264887 21264887

Sequences

>g7115.t124 Gene=g7115 Length=429
GTTTTCATCATGGTTAATCACAGAATTCCATCTGTGTTTTCGAAAACATATGTTACTCCT
AGACGTCCATATGAAAAACCTCGCTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGT
CTCCGTAACAAGCGTGAGGTATGGCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCT
GCTCGTGAATTGCTTACACTTGAAGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCT
CTTCTTCGTCGTCTTGTTCGTATTGTCGTCAACATCCCATCATTTGTCGTTCGTTTGGAC
TCGCAGAAACNCATTGATTTCTCATTGAAGTCACCATTCGGTGGTGGACGACCAGGTCGC
GTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGGTGGCGCTGATGAAGAAGAA
GAGGATTAA

>g7115.t124 Gene=g7115 Length=139
MVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFGLRNKREVWRVKYTLAKIRKAARE
LLTLEEKDEKRLFQGNALLRRLVRIVVNIPSFVVRLDSQKXIDFSLKSPFGGGRPGRVKR
KNMKKGQGGSGGADEEEED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7115.t124 MobiDBLite mobidb-lite consensus disorder prediction 113 139 -
1 g7115.t124 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 8 87 2.5E-51
3 g7115.t124 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 8 87 2.5E-51
2 g7115.t124 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 86 139 2.5E-51
4 g7115.t124 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 86 139 2.5E-51
6 g7115.t124 SMART SM01390 Ribosomal_S4_2 4 83 0.0022
5 g7115.t124 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 12 88 5.47E-11
8 g7115.t124 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 11 85 5.7E-24

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