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.t63 isoform g7115.t63 21263043 21266250
chr_2 g7115 g7115.t63 exon g7115.t63.exon1 21263043 21263273
chr_2 g7115 g7115.t63 TTS g7115.t63 21263047 21263047
chr_2 g7115 g7115.t63 cds g7115.t63.CDS1 21263156 21263273
chr_2 g7115 g7115.t63 exon g7115.t63.exon2 21263772 21263831
chr_2 g7115 g7115.t63 cds g7115.t63.CDS2 21263772 21263831
chr_2 g7115 g7115.t63 exon g7115.t63.exon3 21264028 21264446
chr_2 g7115 g7115.t63 cds g7115.t63.CDS3 21264028 21264446
chr_2 g7115 g7115.t63 exon g7115.t63.exon4 21265812 21266250
chr_2 g7115 g7115.t63 cds g7115.t63.CDS4 21265812 21265871
chr_2 g7115 g7115.t63 TSS g7115.t63 NA NA

Sequences

>g7115.t63 Gene=g7115 Length=1149
GCGGTTGTCGAAGTATTGCTCCAATACGGATTTCTTGAAATTGCTGGCATAATATTGGAT
AGTGCTAGTGATGAACGTTTGATTGAGATTATGCTCGGTATTATAGCTAATATGGGCTGC
ATGAGCGAAACTAGAGAACAACTTTGCGATAATGAGGACGTCATGGCATCTATCCTCAAT
CAACTTTCTAGTAGTGATCCACTTATATTACATCAACTCATGAGGCTATTTCATTCTGCA
ATTCTGTTTGAAAATAAATGCGATGAAAAGATATGGTTTTCTCACTTCCAAAAATGCGAA
AACTTCGTTGAAAAGTTCAGTTATATTTTCGCTAATTCAACTAGTAACACATTGCTAACA
AGTTCCTTTGAAGCTCTAAATGGTATTTGTGCTAAGTTTGCAGCAATTGAATGTCAATCG
GATTCAGAGAAAGACTCAAGTTTTCATCATGGTTAATCACAGAATTCCATCTGTGTTTTC
GAAAACATATGTTACTCCTAGACGTCCATATGAAAAACCTCGCTTGGATGCTGAATTAAG
AGTTATCGGACAATTTGGTCTCCGTAACAAGCGTGAGGTATGGCGAGTCAAGTATACATT
AGCAAAGATCCGTAAAGCTGCTCGTGAATTGCTTACACTTGAAGAGAAAGATGAGAAACG
TTTGTTTCAAGGAAATGCTCTTCTTCGTCGTCTTGTTCGTATTGGTGTGTTAGACGAATC
ACGCATGAAGCTCGATTACGTTCTTGGTTTAAAAATTGAAGATTTCTTAGAACGTCGCTT
GCAGACTCAAGTTTTCAAACTCGGTTTGGCTAAATCTTATCATCATGCTCGCGTTCTTAT
CCGACAAAGACATATTCGCGTTCGTAAACAAGTCGTCAACATCCCATCATTTGTCGTTCG
TTTGGACTCGCAGAAACNCATTGATTTCTCATTGAAGTCACCATTCGGTGGTGGACGACC
AGGTCGCGTCAAGCGAAAGAATATGAAGAAGGGTCAAGGTGGTAGCGGTGGCGCTGATGA
AGAAGAAGAGGATTAAACTGGAATTCACAGCAACATCTTTTCGCAACAAAAAATCTTATT
AAAATCTTTTCCAGTTGGTGTGTGCGATAAAAAAGAACATTCAAACATAATAAATGAAAA
TTGATAAAA

>g7115.t63 Gene=g7115 Length=218
MVFVLSLQQLNVNRIQRKTQVFIMVNHRIPSVFSKTYVTPRRPYEKPRLDAELRVIGQFG
LRNKREVWRVKYTLAKIRKAARELLTLEEKDEKRLFQGNALLRRLVRIGVLDESRMKLDY
VLGLKIEDFLERRLQTQVFKLGLAKSYHHARVLIRQRHIRVRKQVVNIPSFVVRLDSQKX
IDFSLKSPFGGGRPGRVKRKNMKKGQGGSGGADEEEED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g7115.t63 CDD cd00165 S4 132 174 6.39971E-6
5 g7115.t63 Gene3D G3DSA:3.10.290.10 - 133 203 8.9E-11
9 g7115.t63 MobiDBLite mobidb-lite consensus disorder prediction 192 218 -
2 g7115.t63 PANTHER PTHR11831:SF23 40S RIBOSOMAL PROTEIN S9 31 218 1.3E-97
3 g7115.t63 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN 31 218 1.3E-97
1 g7115.t63 Pfam PF01479 S4 domain 132 175 3.6E-9
7 g7115.t63 ProSitePatterns PS00632 Ribosomal protein S4 signature. 130 154 -
11 g7115.t63 ProSiteProfiles PS50889 S4 RNA-binding domain profile. 132 206 9.306
8 g7115.t63 SMART SM01390 Ribosomal_S4_2 27 131 2.3E-17
4 g7115.t63 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 35 184 2.36E-33
10 g7115.t63 TIGRFAM TIGR01018 uS4_arch: ribosomal protein uS4 34 189 1.3E-66

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