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.t64 TTS g9265.t64 1368157 1368157
chr_1 g9265 g9265.t64 isoform g9265.t64 1368266 1369078
chr_1 g9265 g9265.t64 exon g9265.t64.exon1 1368266 1368486
chr_1 g9265 g9265.t64 cds g9265.t64.CDS1 1368268 1368486
chr_1 g9265 g9265.t64 exon g9265.t64.exon2 1368749 1369078
chr_1 g9265 g9265.t64 cds g9265.t64.CDS2 1368749 1369057
chr_1 g9265 g9265.t64 TSS g9265.t64 1369484 1369484

Sequences

>g9265.t64 Gene=g9265 Length=551
GTCTATCATTAATCGTAAATAATGGGTGCGTACAGATACGTTCAAGAGTTATATCGCAAA
AAGCAGAGCGATGTTCTTCGCTATTTGCTTCGAGTTAGATGCTGGCAATATCGTCAATTG
ACTAAATTGCATCGTGCTCCACGTCCATCACGTCCTGATAAAGCACGTCGTCTTGGTTAT
CGTGCAAAGCAAGGATTTTTGATCTATCGCATTCGTGTTCGCCGTGGAGGTCGCAAACGT
CCAGTACACAAGGGATGCACATATGGCAAACCAAAAAGTCATGGTGTTAACCAATTGAAG
CCATACAGAAATTTGCAATCTGTTGCTGAGTCATCTGCATCGATCCATTCCACAATGCTA
TTCGTCGTGATCCTAAAGTTAACTGGATTTGTAATGCTGTTCACAAGCATCGTGAATTAC
GCGGACTTACATCTGCCGGAAAGAGCTCACGCGGTATTGGAAAAGGATACAGATATTCAC
AAACTATTGGTGGCTCACGTCGTGCTGCATGGCGTCGAAAGAATCGCCTCCATCTCCGTC
GCTATCGTTAA

>g9265.t64 Gene=g9265 Length=176
MGAYRYVQELYRKKQSDVLRYLLRVRCWQYRQLTKLHRAPRPSRPDKARRLGYRAKQGFL
IYRIRVRRGGRKRPVHKGCTYGKPKSHGVNQLKPYRNLQSVAESSASIHSTMLFVVILKL
TGFVMLFTSIVNYADLHLPERAHAVLEKDTDIHKLLVAHVVLHGVERIASISVAIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g9265.t64 Gene3D G3DSA:3.40.1120.10 Ribosomal protein l15e 1 168 3.5E-55
2 g9265.t64 PANTHER PTHR11847:SF4 60S RIBOSOMAL PROTEIN L15 1 153 2.4E-52
3 g9265.t64 PANTHER PTHR11847 RIBOSOMAL PROTEIN L15 1 153 2.4E-52
1 g9265.t64 Pfam PF00827 Ribosomal L15 2 114 2.0E-43
7 g9265.t64 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 111 -
8 g9265.t64 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 134 -
6 g9265.t64 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 135 176 -
10 g9265.t64 ProSitePatterns PS01194 Ribosomal protein L15e signature. 46 69 -
11 g9265.t64 SMART SM01384 Ribosomal_L15e_2 2 146 6.3E-43
4 g9265.t64 SUPERFAMILY SSF54189 Ribosomal proteins S24e, L23 and L15e 1 112 3.84E-47
9 g9265.t64 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 112 134 -

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