Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L14.

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_2 g6209 g6209.t20 TSS g6209.t20 15265504 15265504
chr_2 g6209 g6209.t20 isoform g6209.t20 15265527 15269267
chr_2 g6209 g6209.t20 exon g6209.t20.exon1 15265527 15265529
chr_2 g6209 g6209.t20 cds g6209.t20.CDS1 15265527 15265529
chr_2 g6209 g6209.t20 exon g6209.t20.exon2 15265871 15265972
chr_2 g6209 g6209.t20 cds g6209.t20.CDS2 15265871 15265972
chr_2 g6209 g6209.t20 exon g6209.t20.exon3 15266175 15266369
chr_2 g6209 g6209.t20 cds g6209.t20.CDS3 15266175 15266369
chr_2 g6209 g6209.t20 exon g6209.t20.exon4 15266426 15266774
chr_2 g6209 g6209.t20 cds g6209.t20.CDS4 15266426 15266677
chr_2 g6209 g6209.t20 TTS g6209.t20 15266763 15266763
chr_2 g6209 g6209.t20 exon g6209.t20.exon5 15269240 15269267

Sequences

>g6209.t20 Gene=g6209 Length=677
ATGGGTTTTACAAGATTCGTTGAAACCGGACGTATCGCACGTATTTCACGTGGACGCTAC
AAGGGAAAGCTGGTGGCGATTGTTGATGTCATTGATCAGAACAGAGTACTCATCGATGGT
CCATTGACTCGAGTTCCTCGTCAACAATATCCAGTTAGCCATTTACATCTAACAAAGTTT
GTTGTCAAATTTCCATTTACGGCACCAACACGTATTGTGAAAAAAGCTCTAGAGGATTTC
AAGATTAAAGAAAAATGGAGTCAAACACTTTGGGCAGAACGCGCAAAAGCAAAGAGATTG
CGTTCAAATTTGGATGATTTCGAGCGCTTCAAGTTGCGATTAGTTAAGCGTTCAAAGAAT
CGCATGATCGAGCCAGTCTTTTCAAAGCTCAAGAAAGAAGCATCTAAGAACGGCACACTC
TATGGAAAACCTAAAAAGGGAACTAAACCATTGCCACCCAAGAAACCCAAAGTAGAAGGA
GCTAAGAAAAAGAAGAAGGTTAACAAGAAAAAACCTGGCAGTGCTGCAGCAAAGAAGCCA
GCCAAGAAGTAAACATTCATTCTAATGACTTGATAAACATCTGATATAAGGAAATTATGA
AATGAATAAAATCATAATTTTGTTTATTCCTCTTAAATAACTTTAATATTTTTCCCTCTG
TTGATGATCTCGATATG

>g6209.t20 Gene=g6209 Length=183
MGFTRFVETGRIARISRGRYKGKLVAIVDVIDQNRVLIDGPLTRVPRQQYPVSHLHLTKF
VVKFPFTAPTRIVKKALEDFKIKEKWSQTLWAERAKAKRLRSNLDDFERFKLRLVKRSKN
RMIEPVFSKLKKEASKNGTLYGKPKKGTKPLPPKKPKVEGAKKKKKVNKKKPGSAAAKKP
AKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6209.t20 CDD cd06088 KOW_RPL14 7 81 1.46734E-25
8 g6209.t20 Gene3D G3DSA:2.30.30.30 - 1 86 2.7E-34
6 g6209.t20 MobiDBLite mobidb-lite consensus disorder prediction 134 183 -
7 g6209.t20 MobiDBLite mobidb-lite consensus disorder prediction 158 183 -
3 g6209.t20 PANTHER PTHR11127:SF2 60S RIBOSOMAL PROTEIN L14 2 135 1.2E-45
4 g6209.t20 PANTHER PTHR11127 60S RIBOSOMAL PROTEIN L14 2 135 1.2E-45
2 g6209.t20 Pfam PF00467 KOW motif 10 39 8.8E-5
1 g6209.t20 Pfam PF01929 Ribosomal protein L14 46 120 3.0E-24
5 g6209.t20 SUPERFAMILY SSF50104 Translation proteins SH3-like domain 5 95 3.91E-27

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:0003723 RNA binding MF
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