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.t100 TTS g7115.t100 21263047 21263047
chr_2 g7115 g7115.t100 isoform g7115.t100 21263156 21264423
chr_2 g7115 g7115.t100 exon g7115.t100.exon1 21263156 21263254
chr_2 g7115 g7115.t100 cds g7115.t100.CDS1 21263187 21263254
chr_2 g7115 g7115.t100 exon g7115.t100.exon2 21263773 21263831
chr_2 g7115 g7115.t100 cds g7115.t100.CDS2 21263773 21263831
chr_2 g7115 g7115.t100 exon g7115.t100.exon3 21264028 21264423
chr_2 g7115 g7115.t100 cds g7115.t100.CDS3 21264028 21264161
chr_2 g7115 g7115.t100 TSS g7115.t100 21264887 21264887

Sequences

>g7115.t100 Gene=g7115 Length=554
AATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAGACGTCCATATGAAAAACCTCG
CTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCTCCGTAACAAGCGTGAGGTATG
GCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGCTCGTGAATTGCTTACACTTGA
AGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCTTCTTCGTCGTCTTGTTCGTAT
TGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGTTCTTGGTTTAAAAATTGAAGA
TTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACTCGGTTTGGCTAAATCTTATCA
TCATGCTCGCGTTCTTATCCGACAAAGACATATTCGCGTTCGTAAACAAGTCGTCAACAT
CCCATCATTTGTCGTTCGTTTGGACTCGCAGAAACTCACCATTCGGTGGTGGACGACCAG
GTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGGTGGCGCTGATGAAG
AAGAAGAGGATTAA

>g7115.t100 Gene=g7115 Length=86
MKLDYVLGLKIEDFLERRLQTQVFKLGLAKSYHHARVLIRQRHIRVRKQVVNIPSFVVRL
DSQKLTIRWWTTRSRQAKEYEEGSRW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t100 CDD cd00165 S4 17 59 4.58417E-7
5 g7115.t100 Gene3D G3DSA:3.10.290.10 - 16 85 9.0E-12
2 g7115.t100 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 1 65 1.0E-34
3 g7115.t100 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 1 65 1.0E-34
1 g7115.t100 Pfam PF01479 S4 domain 17 60 5.2E-10
7 g7115.t100 ProSitePatterns PS00632 Ribosomal protein S4 signature. 15 39 -
10 g7115.t100 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 17 83 9.584
8 g7115.t100 SMART SM00363 s4_6 17 82 4.3E-5
4 g7115.t100 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 2 67 1.7E-18
9 g7115.t100 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 1 65 2.1E-29

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. There were no conditions that were differentially expressed