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.t91 TTS g9265.t91 1368157 1368157
chr_1 g9265 g9265.t91 isoform g9265.t91 1368266 1369667
chr_1 g9265 g9265.t91 exon g9265.t91.exon1 1368266 1368571
chr_1 g9265 g9265.t91 cds g9265.t91.CDS1 1368266 1368571
chr_1 g9265 g9265.t91 exon g9265.t91.exon2 1368836 1369078
chr_1 g9265 g9265.t91 cds g9265.t91.CDS2 1368836 1369057
chr_1 g9265 g9265.t91 exon g9265.t91.exon3 1369435 1369667
chr_1 g9265 g9265.t91 TSS g9265.t91 NA NA

Sequences

>g9265.t91 Gene=g9265 Length=782
ATGATTAGTTACGATACACACACAAAATTAAAATCTTTTTATTCATCATTTTTGCCCTTT
CAGCTTCAATTTATAAAGAAATTCATTGAGAAATTCTTTGCATTTCGATTGTTAAGTATA
ACGGTTATTTCGTAATTTAAAAAAAGCGTAGTTGTCTTTCAATCCAAAAAACTGCAACTC
GTTCTTTTCGAACAATCCTTCAAAGAGGAAAGGTGTGTTTTCATAAAATTTATGTCTATC
ATTAATCGTAAATAATGGGTGCGTACAGATACGTTCAAGAGTTATATCGCAAAAAGCAGA
GCGATGTTCTTCGCTATTTGCTTCGAGTTAGATGCTGGCAATATCGTCAATTGACTAAAT
TGCATCGTGCTCCACGTCCATCACGTCCTGATAAAGCACGTCGTCTTGGTTATCGTGCAA
AGCAAGGATTTTTGATCTATCGCATTCGTGTTCGCCGTGGAGGTCGCAAACGTCCAGAAC
GTGTTGGTCGACGATTGGGAGGACTTCGTGTTCTCAATTCATACTGGGTCGCACAAGATG
CTGCATTCAAATATTACGAAGTCATCTGCATCGATCCATTCCACAATGCTATTCGTCGTG
ATCCTAAAGTTAACTGGATTTGTAATGCTGTTCACAAGCATCGTGAATTACGCGGACTTA
CATCTGCCGGAAAGAGCTCACGCGGTATTGGAAAAGGATACAGATATTCACAAACTATTG
GTGGCTCACGTCGTGCTGCATGGCGTCGAAAGAATCGCCTCCATCTCCGTCGCTATCGTT
AA

>g9265.t91 Gene=g9265 Length=175
MGAYRYVQELYRKKQSDVLRYLLRVRCWQYRQLTKLHRAPRPSRPDKARRLGYRAKQGFL
IYRIRVRRGGRKRPERVGRRLGGLRVLNSYWVAQDAAFKYYEVICIDPFHNAIRRDPKVN
WICNAVHKHRELRGLTSAGKSSRGIGKGYRYSQTIGGSRRAAWRRKNRLHLRRYR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g9265.t91 Gene3D G3DSA:3.40.1120.10 Ribosomal protein l15e 1 74 3.9E-36
10 g9265.t91 Gene3D G3DSA:3.40.1120.10 Ribosomal protein l15e 75 168 2.1E-44
3 g9265.t91 PANTHER PTHR11847:SF4 60S RIBOSOMAL PROTEIN L15 1 74 9.5E-79
5 g9265.t91 PANTHER PTHR11847 RIBOSOMAL PROTEIN L15 1 74 9.5E-79
4 g9265.t91 PANTHER PTHR11847:SF4 60S RIBOSOMAL PROTEIN L15 75 175 9.5E-79
6 g9265.t91 PANTHER PTHR11847 RIBOSOMAL PROTEIN L15 75 175 9.5E-79
2 g9265.t91 Pfam PF00827 Ribosomal L15 2 74 4.8E-30
1 g9265.t91 Pfam PF00827 Ribosomal L15 75 161 3.6E-40
9 g9265.t91 ProSitePatterns PS01194 Ribosomal protein L15e signature. 46 69 -
8 g9265.t91 SMART SM01384 Ribosomal_L15e_2 2 164 3.0E-100
7 g9265.t91 SUPERFAMILY SSF54189 Ribosomal proteins S24e, L23 and L15e 1 165 7.67E-74

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