Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L23.

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 g11289 g11289.t4 TTS g11289.t4 15429083 15429083
chr_1 g11289 g11289.t4 isoform g11289.t4 15429166 15429885
chr_1 g11289 g11289.t4 exon g11289.t4.exon1 15429166 15429491
chr_1 g11289 g11289.t4 cds g11289.t4.CDS1 15429166 15429491
chr_1 g11289 g11289.t4 exon g11289.t4.exon2 15429554 15429628
chr_1 g11289 g11289.t4 cds g11289.t4.CDS2 15429554 15429628
chr_1 g11289 g11289.t4 exon g11289.t4.exon3 15429873 15429885
chr_1 g11289 g11289.t4 cds g11289.t4.CDS3 15429873 15429885
chr_1 g11289 g11289.t4 TSS g11289.t4 15429913 15429913

Sequences

>g11289.t4 Gene=g11289 Length=414
ATGTCGAAGAGAGGTTCCGCGGGAGGAAAATTCCGTATTTCACTCGGTATGCCTGTTGGC
GCAGTAATTAATTGTGCAGATAATACAGGTGGTAAAAACTTGTATGTTATTGCTGTTCAT
GGCATTCGCGGTCGTTTGAATCGTTTACCTTCAGCTGGTGTTGGTGACATGTTTGTCGCA
ACTGTAAAGAAGGGTAAACCAGAATTGAGAAAGAAAGTAATGCCAGCAGTTGTCATTCGG
CAGCGAAAACCGTTCAGACGACGAGATGGAATCTTTATCTATTTTGAAGATAACGCCGGT
GTAATTGTCAACAATAAAGGTGAAATGAAAGGATCAGCTATTACAGGTCCAGTTGCAAAA
GAGTGTGCAGATTTATGGCCCCGTATTGCATCAAATGCTGGCTCAATAGCCTAA

>g11289.t4 Gene=g11289 Length=137
MSKRGSAGGKFRISLGMPVGAVINCADNTGGKNLYVIAVHGIRGRLNRLPSAGVGDMFVA
TVKKGKPELRKKVMPAVVIRQRKPFRRRDGIFIYFEDNAGVIVNNKGEMKGSAITGPVAK
ECADLWPRIASNAGSIA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11289.t4 Gene3D G3DSA:2.40.150.20 Ribosomal Protein L14; 1 137 6.6E-68
4 g11289.t4 Hamap MF_01367 50S ribosomal protein L14 [rplN]. 16 137 19.220411
2 g11289.t4 PANTHER PTHR11761 50S/60S RIBOSOMAL PROTEIN L14/L23 2 137 1.5E-78
3 g11289.t4 PANTHER PTHR11761:SF22 60S RIBOSOMAL PROTEIN L23 2 137 1.5E-78
1 g11289.t4 Pfam PF00238 Ribosomal protein L14p/L23e 19 135 6.7E-35
7 g11289.t4 ProSitePatterns PS00049 Ribosomal protein L14 signature. 76 102 -
6 g11289.t4 SMART SM01374 Ribosomal_L14_2 16 137 3.8E-58
5 g11289.t4 SUPERFAMILY SSF50193 Ribosomal protein L14 9 135 2.09E-46

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