Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 28S ribosomal protein S9, mitochondrial.

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_1 g11502 g11502.t1 TSS g11502.t1 16669158 16669158
chr_1 g11502 g11502.t1 isoform g11502.t1 16669179 16670825
chr_1 g11502 g11502.t1 exon g11502.t1.exon1 16669179 16669247
chr_1 g11502 g11502.t1 cds g11502.t1.CDS1 16669179 16669247
chr_1 g11502 g11502.t1 exon g11502.t1.exon2 16669312 16669530
chr_1 g11502 g11502.t1 cds g11502.t1.CDS2 16669312 16669530
chr_1 g11502 g11502.t1 exon g11502.t1.exon3 16669587 16669760
chr_1 g11502 g11502.t1 cds g11502.t1.CDS3 16669587 16669760
chr_1 g11502 g11502.t1 exon g11502.t1.exon4 16669819 16669904
chr_1 g11502 g11502.t1 cds g11502.t1.CDS4 16669819 16669904
chr_1 g11502 g11502.t1 exon g11502.t1.exon5 16669956 16670200
chr_1 g11502 g11502.t1 cds g11502.t1.CDS5 16669956 16670200
chr_1 g11502 g11502.t1 exon g11502.t1.exon6 16670343 16670458
chr_1 g11502 g11502.t1 cds g11502.t1.CDS6 16670343 16670458
chr_1 g11502 g11502.t1 exon g11502.t1.exon7 16670772 16670825
chr_1 g11502 g11502.t1 cds g11502.t1.CDS7 16670772 16670825
chr_1 g11502 g11502.t1 TTS g11502.t1 16671646 16671646

Sequences

>g11502.t1 Gene=g11502 Length=963
ATGTTTGCAAAATTAAAACAAAGTTCTCAATTATTTAAATTAACATACAGGACATGTCAG
CCAATTCAAATAAGTAGCAAAAATTACGGAGTAGTAACATCAGAAAAAGATGATTTGTTT
TTACGACGAGATAAAACTAGTAAAGCTATGAAAGCTTATATAGATCGTGCTCAACAACAT
GACGAATTCATGCAAAAACAACGAGAAGAGTTTGAGATTGGAAAGAGGCATTTAGCTAAT
ATGATGGGCGAAGATGCGATTTTATATGAAGATCAAGAAAAAATCGATGAAGCTATTCAA
TATCTGATGCCATCAGCTTTATATGATAAAAGAGCTCGTCCAATGATGAAGCCTCCGGAA
AAAGTTTTTCCTGGTCGAAAAGCGGCTGAATTTGATGAAACTGGTAGACCATATAGCTTT
TTGTTTTATACAGGCAAACCCAACTTCTTTCAATTACTTTATGATGCTGTTGAACATTTA
AATGCTCTTAATAAATTTGAAGATGAGATGATAAGACAGCAAAAGACTGTTGATTTAGCT
TTTAAACTGGAATTAACTGGCTCAGAATGGATTTCTCAAAATCAGTTAGAACTTAAATTA
GTAGAAAGTATTCAACCAGTGGAACATCGATATTTTATTAATACGATGAATCGTTTGGCT
GAGCATCCATATTCGTATCGTGTAAAAGAATTCATTGAACAGTATAGAAAACCTCTTATG
AATCAACAGATTATCTTCGATATTCCAAAACCACAGTTAGATCAAGATGGAAGATTTTTC
ATAACAGTCTATGAATGTCTCCGTAAAAGAGCTCGTGGAGATGTCACTGTCAGATCACCG
GGCACTGGAAAAATATCAATTAATGGTCAACCAATAACATACTTTGAAAATGATCAAAGT
CGAGAACAGATCAGTCCACAAAAAAAATATAACTCACATTGCTCAATTAAACGCTATGAG
TAA

>g11502.t1 Gene=g11502 Length=320
MFAKLKQSSQLFKLTYRTCQPIQISSKNYGVVTSEKDDLFLRRDKTSKAMKAYIDRAQQH
DEFMQKQREEFEIGKRHLANMMGEDAILYEDQEKIDEAIQYLMPSALYDKRARPMMKPPE
KVFPGRKAAEFDETGRPYSFLFYTGKPNFFQLLYDAVEHLNALNKFEDEMIRQQKTVDLA
FKLELTGSEWISQNQLELKLVESIQPVEHRYFINTMNRLAEHPYSYRVKEFIEQYRKPLM
NQQIIFDIPKPQLDQDGRFFITVYECLRKRARGDVTVRSPGTGKISINGQPITYFENDQS
REQISPQKKYNSHCSIKRYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
g11502.t1 PANTHER PTHR21569:SF1 28S RIBOSOMAL PROTEIN S9, MITOCHONDRIAL 47 304 0
g11502.t1 PANTHER PTHR21569 RIBOSOMAL PROTEIN S9 47 304 0

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:0005840 ribosome CC
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome 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