Gene loci information

Transcript annotation

  • This transcript has been annotated as 39S ribosomal protein L22, 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_2 g8398 g8398.t5 isoform g8398.t5 30151975 30153338
chr_2 g8398 g8398.t5 exon g8398.t5.exon1 30151975 30152527
chr_2 g8398 g8398.t5 cds g8398.t5.CDS1 30152518 30152527
chr_2 g8398 g8398.t5 exon g8398.t5.exon2 30152583 30152799
chr_2 g8398 g8398.t5 cds g8398.t5.CDS2 30152583 30152799
chr_2 g8398 g8398.t5 exon g8398.t5.exon3 30152860 30153073
chr_2 g8398 g8398.t5 cds g8398.t5.CDS3 30152860 30153073
chr_2 g8398 g8398.t5 exon g8398.t5.exon4 30153132 30153338
chr_2 g8398 g8398.t5 cds g8398.t5.CDS4 30153132 30153338
chr_2 g8398 g8398.t5 TSS g8398.t5 30153376 30153376
chr_2 g8398 g8398.t5 TTS g8398.t5 NA NA

Sequences

>g8398.t5 Gene=g8398 Length=1191
ATGCTAAATTTACTAAAAACTTCAAGTTTATTGATAAGAAATGAAGTGAATTTGATAAAT
TCTCAAATTGGCGCATTATTCCATACATCAACAGTTGTTGATGCAAAGAATAGCAATGCA
GGACACAGTAATAAACCAAAAAGATTTTTAAGACAAAATAAGAAAATTTTTGAGCCACAA
TTACCAGATGAAACACCGAGACCAGCATTCGTTTGTCATCAAAAAGAGAACATTCGATAT
AGTCCTAAGAAAATGTGGTACATTGCGGCATTTGTGCGAGGAATGACTGTAGATGAAGCT
GTGAAGCAATTAAGCTTTCAACTTAAAAAAGGTGCTGCAGCTGTTAAAGAAACGCTTTTA
GAAGCTCAAGAGATTGCTGTCAAACAGCACAATGTTGAATTCAAAAGTAATTTGTGGATC
TCCGAATCATTTGTTGGTAAAGGAGTAGTCTTTAAAGGAATTAGACGACATGCAAAAGGT
AGAATGGGAAGAGTAGAATATAAACATTGTCACTATTTCGTAAAGCTCGAAGAAGGAACA
CCTCCGGAACATTATTATTTGCCTTATCCTAAAACACCAGAGCAACAACTTGATGATTGG
ATGAGTCAAATGAGAAAGAGAAAAATAACGAATTCATTACTCTGCTGACTCGCGTATCAT
TGGAAGACATTCATCAATTAAATCTTCAACTTTAGTGTGCATTTGAATTCCAACTAAGAC
TGCAAACTTTGGTTTCTTTAATAATTGAGCTCGATCTGGATCTGAATGTGCTTCCATGTG
AAGATCAAGTTTCTGTTTTGTTGATAATTTACTTTTGCATATTGAACACATAAAATGCTT
TCCTTCATGTTTTGAACGAATATGGGCAGTCAAGTTCTTTTTAGCATTATAAAATTTTCC
ACAATTCTCAAAATGACACTCAAACACTTCAGTTTGTTTCTGCATATGCACATTCATATG
AATCTTGAGATTTTGTTTGATTGAAAATTGTTTTGCACATAAATCACAAATAAATCGTTT
CTCTTCCGTATTTGAATTACGACAAACTCGACGATGTTTAACAAACATTGTCCAATTTGG
AAGGACTTTGTTACAATCATTACAAATTCGCTCTTTTATCTTATGAACCGATGCTACATG
CTTATGATAAATGTTGTTATTGAAAAATCCTTCATTACATTCTTCACATGT

>g8398.t5 Gene=g8398 Length=215
MLNLLKTSSLLIRNEVNLINSQIGALFHTSTVVDAKNSNAGHSNKPKRFLRQNKKIFEPQ
LPDETPRPAFVCHQKENIRYSPKKMWYIAAFVRGMTVDEAVKQLSFQLKKGAAAVKETLL
EAQEIAVKQHNVEFKSNLWISESFVGKGVVFKGIRRHAKGRMGRVEYKHCHYFVKLEEGT
PPEHYYLPYPKTPEQQLDDWMSQMRKRKITNSLLC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g8398.t5 CDD cd00336 Ribosomal_L22 71 176 0
5 g8398.t5 Gene3D G3DSA:3.90.470.10 Ribosomal Protein L22; Chain A 46 213 0
2 g8398.t5 PANTHER PTHR13501:SF8 39S RIBOSOMAL PROTEIN L22, MITOCHONDRIAL 42 207 0
3 g8398.t5 PANTHER PTHR13501 CHLOROPLAST 50S RIBOSOMAL PROTEIN L22-RELATED 42 207 0
1 g8398.t5 Pfam PF00237 Ribosomal protein L22p/L17e 74 176 0
4 g8398.t5 SUPERFAMILY SSF54843 Ribosomal protein L22 62 180 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:0015934 large ribosomal subunit 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