Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L15.

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 g9265 g9265.t55 TTS g9265.t55 1368157 1368157
chr_1 g9265 g9265.t55 isoform g9265.t55 1368172 1369667
chr_1 g9265 g9265.t55 exon g9265.t55.exon1 1368172 1368571
chr_1 g9265 g9265.t55 cds g9265.t55.CDS1 1368266 1368571
chr_1 g9265 g9265.t55 exon g9265.t55.exon2 1368749 1369078
chr_1 g9265 g9265.t55 cds g9265.t55.CDS2 1368749 1369057
chr_1 g9265 g9265.t55 exon g9265.t55.exon3 1369444 1369667
chr_1 g9265 g9265.t55 TSS g9265.t55 NA NA

Sequences

>g9265.t55 Gene=g9265 Length=954
ATGATTAGTTACGATACACACACAAAATTAAAATCTTTTTATTCATCATTTTTGCCCTTT
CAGCTTCAATTTATAAAGAAATTCATTGAGAAATTCTTTGCATTTCGATTGTTAAGTATA
ACGGTTATTTCGTAATTTAAAAAAAGCGTAGTTGTCTTTCAATCCAAAAAACTGCAACTC
GTTCTTTTCGAACAATCCTTCAAAGAGGAAAGGTGTGTTTTCATGTCTATCATTAATCGT
AAATAATGGGTGCGTACAGATACGTTCAAGAGTTATATCGCAAAAAGCAGAGCGATGTTC
TTCGCTATTTGCTTCGAGTTAGATGCTGGCAATATCGTCAATTGACTAAATTGCATCGTG
CTCCACGTCCATCACGTCCTGATAAAGCACGTCGTCTTGGTTATCGTGCAAAGCAAGGAT
TTTTGATCTATCGCATTCGTGTTCGCCGTGGAGGTCGCAAACGTCCAGTACACAAGGGAT
GCACATATGGCAAACCAAAAAGTCATGGTGTTAACCAATTGAAGCCATACAGAAATTTGC
AATCTGTTGCTGAGGAACGTGTTGGTCGACGATTGGGAGGACTTCGTGTTCTCAATTCAT
ACTGGGTCGCACAAGATGCTGCATTCAAATATTACGAAGTCATCTGCATCGATCCATTCC
ACAATGCTATTCGTCGTGATCCTAAAGTTAACTGGATTTGTAATGCTGTTCACAAGCATC
GTGAATTACGCGGACTTACATCTGCCGGAAAGAGCTCACGCGGTATTGGAAAAGGATACA
GATATTCACAAACTATTGGTGGCTCACGTCGTGCTGCATGGCGTCGAAAGAATCGCCTCC
ATCTCCGTCGCTATCGTTAAAATGGAAATACACATTAAATCGATTTATTTTGTGTATATT
GTTATAAACATCTTAACAATTTTTTTCAAAAATGAATAAATTTCATATATCAAA

>g9265.t55 Gene=g9265 Length=204
MGAYRYVQELYRKKQSDVLRYLLRVRCWQYRQLTKLHRAPRPSRPDKARRLGYRAKQGFL
IYRIRVRRGGRKRPVHKGCTYGKPKSHGVNQLKPYRNLQSVAEERVGRRLGGLRVLNSYW
VAQDAAFKYYEVICIDPFHNAIRRDPKVNWICNAVHKHRELRGLTSAGKSSRGIGKGYRY
SQTIGGSRRAAWRRKNRLHLRRYR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9265.t55 Gene3D G3DSA:3.40.1120.10 Ribosomal protein l15e 1 197 2.6E-104
2 g9265.t55 PANTHER PTHR11847:SF4 60S RIBOSOMAL PROTEIN L15 1 204 1.5E-100
3 g9265.t55 PANTHER PTHR11847 RIBOSOMAL PROTEIN L15 1 204 1.5E-100
1 g9265.t55 Pfam PF00827 Ribosomal L15 2 190 1.4E-88
6 g9265.t55 ProSitePatterns PS01194 Ribosomal protein L15e signature. 46 69 -
5 g9265.t55 SMART SM01384 Ribosomal_L15e_2 2 193 2.5E-133
4 g9265.t55 SUPERFAMILY SSF54189 Ribosomal proteins S24e, L23 and L15e 1 194 8.15E-90

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. There were no conditions that were differentially expressed