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.t64 isoform g7115.t64 21263044 21264356
chr_2 g7115 g7115.t64 exon g7115.t64.exon1 21263044 21263270
chr_2 g7115 g7115.t64 TTS g7115.t64 21263047 21263047
chr_2 g7115 g7115.t64 cds g7115.t64.CDS1 21263268 21263270
chr_2 g7115 g7115.t64 exon g7115.t64.exon2 21263780 21263831
chr_2 g7115 g7115.t64 cds g7115.t64.CDS2 21263780 21263831
chr_2 g7115 g7115.t64 exon g7115.t64.exon3 21264028 21264356
chr_2 g7115 g7115.t64 cds g7115.t64.CDS3 21264028 21264161
chr_2 g7115 g7115.t64 TSS g7115.t64 21264887 21264887

Sequences

>g7115.t64 Gene=g7115 Length=608
GCTGAATTAAGAGTTATCGGACAATTTGGTCTCCGTAACAAGCGTGAGGTATGGCGAGTC
AAGTATACATTAGCAAAGATCCGTAAAGCTGCTCGTGAATTGCTTACACTTGAAGAGAAA
GATGAGAAACGTTTGTTTCAAGGAAATGCTCTTCTTCGTCGTCTTGTTCGTATTGGTGTG
TTAGACGAATCACGCATGAAGCTCGATTACGTTCTTGGTTTAAAAATTGAAGATTTCTTA
GAACGTCGCTTGCAGACTCAAGTTTTCAAACTCGGTTTGGCTAAATCTTATCATCATGCT
CGCGTTCTTATCCGACAAAGACATATTCGCGTTCGTAAACAAGTCGTCAACATCCCATCA
TTTGTCGTTCGTTTGGACTCGTGATTTCTCATTGAAGTCACCATTCGGTGGTGGACGACC
AGGTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGGTGGCGCTGATGA
AGAAGAAGAGGATTAAACTGGAATTCACAGCAACATCTTTTCGCAACAAAAAATCTTATT
AAAATCTTTTCCAGTTGGTGTGTGCGATAAAAAAGAACATTCAAACATAATAAATGAAAA
TTGATAAA

>g7115.t64 Gene=g7115 Length=62
MKLDYVLGLKIEDFLERRLQTQVFKLGLAKSYHHARVLIRQRHIRVRKQVVNIPSFVVRL
DS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7115.t64 CDD cd00165 S4 17 59 2.57838E-6
6 g7115.t64 Gene3D G3DSA:3.10.290.10 - 16 62 2.6E-11
2 g7115.t64 PANTHER PTHR11831:SF5 40S RIBOSOMAL PROTEIN S9 1 62 3.7E-33
3 g7115.t64 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 1 62 3.7E-33
1 g7115.t64 Pfam PF01479 S4 domain 17 59 2.4E-10
5 g7115.t64 ProSitePatterns PS00632 Ribosomal protein S4 signature. 15 39 -
4 g7115.t64 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 2 60 2.59E-18
7 g7115.t64 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 1 61 1.8E-28

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: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.

Raw TPM values