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.t27 isoform g7115.t27 21263043 21264423
chr_2 g7115 g7115.t27 exon g7115.t27.exon1 21263043 21263266
chr_2 g7115 g7115.t27 TTS g7115.t27 21263047 21263047
chr_2 g7115 g7115.t27 cds g7115.t27.CDS1 21263156 21263266
chr_2 g7115 g7115.t27 exon g7115.t27.exon2 21263768 21263831
chr_2 g7115 g7115.t27 cds g7115.t27.CDS2 21263768 21263831
chr_2 g7115 g7115.t27 exon g7115.t27.exon3 21264028 21264423
chr_2 g7115 g7115.t27 cds g7115.t27.CDS3 21264028 21264161
chr_2 g7115 g7115.t27 TSS g7115.t27 21264887 21264887

Sequences

>g7115.t27 Gene=g7115 Length=684
AATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAGACGTCCATATGAAAAACCTCG
CTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCTCCGTAACAAGCGTGAGGTATG
GCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGCTCGTGAATTGCTTACACTTGA
AGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCTTCTTCGTCGTCTTGTTCGTAT
TGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGTTCTTGGTTTAAAAATTGAAGA
TTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACTCGGTTTGGCTAAATCTTATCA
TCATGCTCGCGTTCTTATCCGACAAAGACATATTCGCGTTCGTAAACAAGTCGTCAACAT
CCCATCATTTGTCGTTCGTTTGGACTCGCAGAAACNNNNNTTCTCATTGAAGTCACCATT
CGGTGGTGGACGACCAGGTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAG
CGGTGGCGCTGATGAAGAAGAAGAGGATTAAACTGGAATTCACAGCAACATCTTTTCGCA
ACAAAAAATCTTATTAAAATCTTTTCCAGTTGGTGTGTGCGATAAAAAAGAACATTCAAA
CATAATAAATGAAAATTGATAAAA

>g7115.t27 Gene=g7115 Length=102
MKLDYVLGLKIEDFLERRLQTQVFKLGLAKSYHHARVLIRQRHIRVRKQVVNIPSFVVRL
DSQKXXFSLKSPFGGGRPGRVKRKNMKKGQGGSGGADEEEED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t27 CDD cd00165 S4 17 59 4.59631E-7
5 g7115.t27 Gene3D G3DSA:3.10.290.10 - 18 74 3.3E-11
8 g7115.t27 MobiDBLite mobidb-lite consensus disorder prediction 69 102 -
2 g7115.t27 PANTHER PTHR11831:SF27 - 2 102 1.3E-51
3 g7115.t27 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 2 102 1.3E-51
1 g7115.t27 Pfam PF01479 S4 domain 17 60 8.0E-10
7 g7115.t27 ProSitePatterns PS00632 Ribosomal protein S4 signature. 15 39 -
10 g7115.t27 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 17 90 9.048
4 g7115.t27 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 2 61 6.93E-18
9 g7115.t27 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 1 73 1.1E-30

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