Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t99 TTS g9265.t99 1368157 1368157
chr_1 g9265 g9265.t99 isoform g9265.t99 1368266 1369667
chr_1 g9265 g9265.t99 exon g9265.t99.exon1 1368266 1368571
chr_1 g9265 g9265.t99 cds g9265.t99.CDS1 1368268 1368571
chr_1 g9265 g9265.t99 exon g9265.t99.exon2 1368783 1369078
chr_1 g9265 g9265.t99 cds g9265.t99.CDS2 1368783 1369057
chr_1 g9265 g9265.t99 exon g9265.t99.exon3 1369217 1369237
chr_1 g9265 g9265.t99 exon g9265.t99.exon4 1369456 1369667
chr_1 g9265 g9265.t99 TSS g9265.t99 NA NA

Sequences

>g9265.t99 Gene=g9265 Length=835
ATGATTAGTTACGATACACACACAAAATTAAAATCTTTTTATTCATCATTTTTGCCCTTT
CAGCTTCAATTTATAAAGAAATTCATTGAGAAATTCTTTGCATTTCGATTGTTAAGTATA
ACGGTTATTTCGTAATTTAAAAAAAGCGTAGTTGTCTTTCAATCCAAAAAACTGCAACTC
GTTCTTTTCGAACAATCCTTCAAAGAGGAAAGATAGACGATTTATAAATACAGGTCTATC
ATTAATCGTAAATAATGGGTGCGTACAGATACGTTCAAGAGTTATATCGCAAAAAGCAGA
GCGATGTTCTTCGCTATTTGCTTCGAGTTAGATGCTGGCAATATCGTCAATTGACTAAAT
TGCATCGTGCTCCACGTCCATCACGTCCTGATAAAGCACGTCGTCTTGGTTATCGTGCAA
AGCAAGGATTTTTGATCTATCGCATTCGTGTTCGCCGTGGAGGTCGCAAACGTCCAGTAC
ACAAGGGATGCACATATGGCAAACCAAAAAGTCATGGTGTTAACCAATTGAACGTGTTGG
TCGACGATTGGGAGGACTTCGTGTTCTCAATTCATACTGGGTCGCACAAGATGCTGCATT
CAAATATTACGAAGTCATCTGCATCGATCCATTCCACAATGCTATTCGTCGTGATCCTAA
AGTTAACTGGATTTGTAATGCTGTTCACAAGCATCGTGAATTACGCGGACTTACATCTGC
CGGAAAGAGCTCACGCGGTATTGGAAAAGGATACAGATATTCACAAACTATTGGTGGCTC
ACGTCGTGCTGCATGGCGTCGAAAGAATCGCCTCCATCTCCGTCGCTATCGTTAA

>g9265.t99 Gene=g9265 Length=193
MGAYRYVQELYRKKQSDVLRYLLRVRCWQYRQLTKLHRAPRPSRPDKARRLGYRAKQGFL
IYRIRVRRGGRKRPVHKGCTYGKPKSHGVNQLNVLVDDWEDFVFSIHTGSHKMLHSNITK
SSASIHSTMLFVVILKLTGFVMLFTSIVNYADLHLPERAHAVLEKDTDIHKLLVAHVVLH
GVERIASISVAIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g9265.t99 Gene3D G3DSA:3.40.1120.10 Ribosomal protein l15e 1 97 2.3E-47
2 g9265.t99 PANTHER PTHR11847:SF4 60S RIBOSOMAL PROTEIN L15 1 93 1.1E-45
3 g9265.t99 PANTHER PTHR11847 RIBOSOMAL PROTEIN L15 1 93 1.1E-45
1 g9265.t99 Pfam PF00827 Ribosomal L15 2 93 2.3E-36
6 g9265.t99 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 128 -
8 g9265.t99 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -
7 g9265.t99 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 152 193 -
10 g9265.t99 ProSitePatterns PS01194 Ribosomal protein L15e signature. 46 69 -
11 g9265.t99 SMART SM01384 Ribosomal_L15e_2 2 130 2.2E-33
4 g9265.t99 SUPERFAMILY SSF54189 Ribosomal proteins S24e, L23 and L15e 1 94 7.67E-40
9 g9265.t99 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -

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.

Raw TPM values