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.t22 isoform g7115.t22 21263043 21264409
chr_2 g7115 g7115.t22 exon g7115.t22.exon1 21263043 21263262
chr_2 g7115 g7115.t22 TTS g7115.t22 21263047 21263047
chr_2 g7115 g7115.t22 cds g7115.t22.CDS1 21263156 21263262
chr_2 g7115 g7115.t22 exon g7115.t22.exon2 21263767 21263831
chr_2 g7115 g7115.t22 cds g7115.t22.CDS2 21263767 21263831
chr_2 g7115 g7115.t22 exon g7115.t22.exon3 21264028 21264409
chr_2 g7115 g7115.t22 cds g7115.t22.CDS3 21264028 21264161
chr_2 g7115 g7115.t22 TSS g7115.t22 21264887 21264887

Sequences

>g7115.t22 Gene=g7115 Length=667
TTTCGAAAACATATGTTACTCCTAGACGTCCATATGAAAAACCTCGCTTGGATGCTGAAT
TAAGAGTTATCGGACAATTTGGTCTCCGTAACAAGCGTGAGGTATGGCGAGTCAAGTATA
CATTAGCAAAGATCCGTAAAGCTGCTCGTGAATTGCTTACACTTGAAGAGAAAGATGAGA
AACGTTTGTTTCAAGGAAATGCTCTTCTTCGTCGTCTTGTTCGTATTGGTGTGTTAGACG
AATCACGCATGAAGCTCGATTACGTTCTTGGTTTAAAAATTGAAGATTTCTTAGAACGTC
GCTTGCAGACTCAAGTTTTCAAACTCGGTTTGGCTAAATCTTATCATCATGCTCGCGTTC
TTATCCGACAAAGACATATTCGCGTTCGTAAACAAGTCGTCAACATCCCATCATTTGTCG
TTCGTTTGGACTCGCAGAAACNNNNNNCATTGAAGTCACCATTCGGTGGTGGACGACCAG
GTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGGTGGCGCTGATGAAG
AAGAAGAGGATTAAACTGGAATTCACAGCAACATCTTTTCGCAACAAAAAATCTTATTAA
AATCTTTTCCAGTTGGTGTGTGCGATAAAAAAGAACATTCAAACATAATAAATGAAAATT
GATAAAA

>g7115.t22 Gene=g7115 Length=101
MKLDYVLGLKIEDFLERRLQTQVFKLGLAKSYHHARVLIRQRHIRVRKQVVNIPSFVVRL
DSQKXXXLKSPFGGGRPGRVKRKNMKKGQGGSGGADEEEED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t22 CDD cd00165 S4 17 59 6.44102E-7
5 g7115.t22 Gene3D G3DSA:3.10.290.10 - 16 71 3.3E-11
8 g7115.t22 MobiDBLite mobidb-lite consensus disorder prediction 68 101 -
2 g7115.t22 PANTHER PTHR11831:SF27 - 2 101 1.9E-50
3 g7115.t22 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 2 101 1.9E-50
1 g7115.t22 Pfam PF01479 S4 domain 17 60 7.8E-10
7 g7115.t22 ProSitePatterns PS00632 Ribosomal protein S4 signature. 15 39 -
4 g7115.t22 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 2 61 7.85E-18
9 g7115.t22 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 1 66 1.8E-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.

Raw TPM values