Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L18.

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 g11017 g11017.t11 TTS g11017.t11 13420777 13420777
chr_1 g11017 g11017.t11 isoform g11017.t11 13420889 13421629
chr_1 g11017 g11017.t11 exon g11017.t11.exon1 13420889 13421089
chr_1 g11017 g11017.t11 cds g11017.t11.CDS1 13420889 13421089
chr_1 g11017 g11017.t11 exon g11017.t11.exon2 13421174 13421368
chr_1 g11017 g11017.t11 cds g11017.t11.CDS2 13421174 13421302
chr_1 g11017 g11017.t11 exon g11017.t11.exon3 13421542 13421629
chr_1 g11017 g11017.t11 TSS g11017.t11 13421778 13421778

Sequences

>g11017.t11 Gene=g11017 Length=484
GGGCAAGGACATTAGTCATAAGTGGGACAGAAAAGTCCGCAGAACATCTCCAAAATCATT
GGATGTTTACTTGCGTCTTTTAGTGAAGCTTTATCGCTTCCTGTATCGCAGAACTCATCA
GAAGTTCAATAAAATCATTCTGCGACGTTTATTCATGAGTAAAATCAACCGCCCAGTGAT
TTCGTTGCAACGCGTAATCCGTTTGATGAAACAACGTCAAGCAAAGGAAAACACAATTGC
AGTTATTGTTGGCAAAGTTACAAATGACTTGAGAATTTTGGAATTCGATCAATTGGCATT
GCTCGCACCTACTGGCAAAAACACAATCTTGATGCAAGGTAAACGCAATAATCGTGAGGC
CGTAACACACTTTGGAAAAGCTCCTGGTGTACCTCATTCCCATACAAGACCATACGTTCG
ATCAAAAGGACGTAAATTCGAACGCGCTCGTGGTCGCAGAACATCATGCGGATACAAGAA
GTAA

>g11017.t11 Gene=g11017 Length=109
MSKINRPVISLQRVIRLMKQRQAKENTIAVIVGKVTNDLRILEFDQLALLAPTGKNTILM
QGKRNNREAVTHFGKAPGVPHSHTRPYVRSKGRKFERARGRRTSCGYKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11017.t11 Gene3D G3DSA:3.100.10.10 - 1 41 1.2E-10
7 g11017.t11 Gene3D G3DSA:3.100.10.10 - 42 109 2.3E-32
6 g11017.t11 MobiDBLite mobidb-lite consensus disorder prediction 90 109 -
3 g11017.t11 PANTHER PTHR10934 60S RIBOSOMAL PROTEIN L18 1 43 1.0E-37
5 g11017.t11 PANTHER PTHR10934:SF5 CYTOPLASMIC RIBOSOMAL PROTEIN L18 1 43 1.0E-37
2 g11017.t11 PANTHER PTHR10934 60S RIBOSOMAL PROTEIN L18 42 108 1.0E-37
4 g11017.t11 PANTHER PTHR10934:SF5 CYTOPLASMIC RIBOSOMAL PROTEIN L18 42 108 1.0E-37
1 g11017.t11 Pfam PF17135 Ribosomal protein 60S L18 and 50S L18e 41 109 6.5E-31

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed