Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t11 isoform g7115.t11 21263038 21264444
chr_2 g7115 g7115.t11 exon g7115.t11.exon1 21263038 21263116
chr_2 g7115 g7115.t11 TTS g7115.t11 21263047 21263047
chr_2 g7115 g7115.t11 cds g7115.t11.CDS1 21263082 21263116
chr_2 g7115 g7115.t11 exon g7115.t11.exon2 21263185 21263273
chr_2 g7115 g7115.t11 cds g7115.t11.CDS2 21263185 21263273
chr_2 g7115 g7115.t11 exon g7115.t11.exon3 21263772 21263831
chr_2 g7115 g7115.t11 cds g7115.t11.CDS3 21263772 21263831
chr_2 g7115 g7115.t11 exon g7115.t11.exon4 21264028 21264444
chr_2 g7115 g7115.t11 cds g7115.t11.CDS4 21264028 21264437
chr_2 g7115 g7115.t11 TSS g7115.t11 21264887 21264887

Sequences

>g7115.t11 Gene=g7115 Length=645
TTTCATCATGGTTAATCACAGAATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAG
ACGTCCATATGAAAAACCTCGCTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCT
CCGTAACAAGCGTGAGGTATGGCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGC
TCGTGAATTGCTTACACTTGAAGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCT
TCTTCGTCGTCTTGTTCGTATTGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGT
TCTTGGTTTAAAAATTGAAGATTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACT
CGGTTTGGCTAAATCTTATCATCATGCTCGCGTTCTTATCCGACAAAGACATATTCGCGT
TCGTAAACAAGTCGTCAACATCCCATCATTTGTCGTTCGTTTGGACTCGCAGAAACNCAT
TGATTTCTCATTGAAGTCACCATTCGGTGGTGGACGACCAGGTCGCGTCAAGCGAAAGAA
TATGAAGAAGGGTCAAGGTGGTAGCGTTATTAAAATCTTTTCCAGTTGGTGTGTGCGATA
AAAAAGAACATTCAAACATAATAAATGAAAATTGATAAAAAAAAG

>g7115.t11 Gene=g7115 Length=197
MVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFGLRNKREVWRVKYTLAKIRKAARE
LLTLEEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL
AKSYHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKXIDFSLKSPFGGGRPGRVKRKNMK
KGQGGSVIKIFSSWCVR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t11 CDD cd00165 S4 109 151 6.79128E-6
5 g7115.t11 Gene3D G3DSA:3.10.290.10 - 110 182 6.7E-11
2 g7115.t11 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 8 186 2.0E-93
3 g7115.t11 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 8 186 2.0E-93
1 g7115.t11 Pfam PF01479 S4 domain 109 152 3.0E-9
7 g7115.t11 ProSitePatterns PS00632 Ribosomal protein S4 signature. 107 131 -
10 g7115.t11 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 109 183 9.306
8 g7115.t11 SMART SM01390 Ribosomal_S4_2 4 108 2.3E-17
4 g7115.t11 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 12 162 2.14E-33
9 g7115.t11 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 11 166 9.3E-67

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

Pathway

  • This transcript belongs to the following pathways

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