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.t74 TTS g7115.t74 21263047 21263047
chr_2 g7115 g7115.t74 isoform g7115.t74 21263050 21264443
chr_2 g7115 g7115.t74 exon g7115.t74.exon1 21263050 21263269
chr_2 g7115 g7115.t74 cds g7115.t74.CDS1 21263187 21263269
chr_2 g7115 g7115.t74 exon g7115.t74.exon2 21263779 21263831
chr_2 g7115 g7115.t74 cds g7115.t74.CDS2 21263779 21263831
chr_2 g7115 g7115.t74 exon g7115.t74.exon3 21264028 21264443
chr_2 g7115 g7115.t74 cds g7115.t74.CDS3 21264028 21264437
chr_2 g7115 g7115.t74 TSS g7115.t74 21264887 21264887

Sequences

>g7115.t74 Gene=g7115 Length=689
TTCATCATGGTTAATCACAGAATTCCATCTGTGTTTTCGAAAACATATGTTACTCCTAGA
CGTCCATATGAAAAACCTCGCTTGGATGCTGAATTAAGAGTTATCGGACAATTTGGTCTC
CGTAACAAGCGTGAGGTATGGCGAGTCAAGTATACATTAGCAAAGATCCGTAAAGCTGCT
CGTGAATTGCTTACACTTGAAGAGAAAGATGAGAAACGTTTGTTTCAAGGAAATGCTCTT
CTTCGTCGTCTTGTTCGTATTGGTGTGTTAGACGAATCACGCATGAAGCTCGATTACGTT
CTTGGTTTAAAAATTGAAGATTTCTTAGAACGTCGCTTGCAGACTCAAGTTTTCAAACTC
GGTTTGGCTAAATCTTATCATCATGCTCGCGTTCTTATCCGACAAAGACATATTCGCGTT
CGTAAACAAGTCGTCAACATCCCATCATTTGTCGTTCGTTTGGACTCGCGATTTCTCATT
GAAGTCACCATTCGGTGGTGGACGACCAGGTCGCGTCAAGCGAAAGAATATGAAGAAGGG
TCAAGGTGGTAGCGGTGGCGCTGATGAAGAAGAAGAGGATTAAACTGGAATTCACAGCAA
CATCTTTTCGCAACAAAAAATCTTATTAAAATCTTTTCCAGTTGGTGTGTGCGATAAAAA
AGAACATTCAAACATAATAAATGAAAATT

>g7115.t74 Gene=g7115 Length=181
MVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFGLRNKREVWRVKYTLAKIRKAARE
LLTLEEKDEKRLFQGNALLRRLVRIGVLDESRMKLDYVLGLKIEDFLERRLQTQVFKLGL
AKSYHHARVLIRQRHIRVRKQVVNIPSFVVRLDSRFLIEVTIRWWTTRSRQAKEYEEGSR
W

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t74 CDD cd00165 S4 109 151 4.8511E-6
5 g7115.t74 Gene3D G3DSA:3.10.290.10 - 110 177 6.0E-11
2 g7115.t74 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 8 170 5.1E-77
3 g7115.t74 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 8 170 5.1E-77
1 g7115.t74 Pfam PF01479 S4 domain 109 152 3.7E-9
7 g7115.t74 ProSitePatterns PS00632 Ribosomal protein S4 signature. 107 131 -
11 g7115.t74 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 109 178 9.312
9 g7115.t74 SMART SM01390 Ribosomal_S4_2 4 108 2.3E-17
8 g7115.t74 SMART SM00363 s4_6 109 177 8.7E-4
4 g7115.t74 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 12 157 5.78E-33
10 g7115.t74 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 11 159 3.4E-61

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