Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L4.

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_3 g3343 g3343.t40 TTS g3343.t40 24752884 24752884
chr_3 g3343 g3343.t40 isoform g3343.t40 24753005 24754773
chr_3 g3343 g3343.t40 exon g3343.t40.exon1 24753005 24753432
chr_3 g3343 g3343.t40 cds g3343.t40.CDS1 24753393 24753432
chr_3 g3343 g3343.t40 exon g3343.t40.exon2 24753948 24754053
chr_3 g3343 g3343.t40 cds g3343.t40.CDS2 24753948 24754053
chr_3 g3343 g3343.t40 exon g3343.t40.exon3 24754107 24754773
chr_3 g3343 g3343.t40 cds g3343.t40.CDS3 24754107 24754398
chr_3 g3343 g3343.t40 TSS g3343.t40 24754851 24754851

Sequences

>g3343.t40 Gene=g3343 Length=1201
ATGGTTAGTATTTGTAAATATTCATTAGTTAATTGCATAAAGTTGCGTGTGCATATCGAT
TTTGTGCAATTACTGAGCGTTTAAATTGAAAAAATTAGGAAAAATATTTTTAATAATTTT
TGCATGTGGCAAATAGTAATTTTGACTATTTTCTATTGTTTCCAGCACTAAAATCGTTGC
ACAAACTTAAAGATAAATCATATAAAAATGTATTTTAATTGATATTTCTTTTAATTTTAG
AGTAAATCAGCTGCTCGTCCGCTCGTCAGTGTTTATACTGACAAAAGTGAGGTTATTAAA
GATACAACAATTCCATTGCCTGCAATTTTCAAGGCTCCAATTCGCCCAGATGTCGTCAAT
GATGTACATCAATTAATGCGTCGTAATGCTCGTCAAGCATACGCTGTTAGCGCTGAAGCA
GGCCATCAAACATCAGCTGAATCATGGGGTACAGGTCGTGCTGTTGCTCGTATTCCTCGA
GTTCGTGGTGGTGGTACTCATCGTTCAGGTCAGGGTGCTTTCGGAAATATGTGTCGTGGA
GGTCGCATGTTCGCTCCAACTAAACCATGGCGTAGATGGCATCGTCGCATTAATGTCAAC
TTGAAACGTTATGCAGTTGTTTCAGCTGTTGCTGCATCAGGCGTTCCAGCTCTTGTTCAA
GCTCGAGGACATATTATTGACGGAATTGCTGAACTTCCATTGGTTGTCTCAGATAAAGTT
CAAGAATACAACAAGACCAAACAAGCTGTTTTGTTCTTACGTCGTAACAAGTTTGAAAAA
GGCTTACAATCTGCCACATCCAATTATGTCTAACACTGATTTGACTCGCTTGCTCAAATC
ACAAGAAATCAAGAGCGTTTTGAATGCACCTAAGAAGAGAGTTTTCCATCGTGTACGCCG
CTTGAATCCATTGAAGAACGCCAGACAAAAGACCAAGTTGAATCCATATTCAGAAGTTAC
TCGTCGTCGTGCATTGTTGGCTAAAGAAAAGCGAAAGTATGAGACACAAATTGCCAAGGC
AAAGAAGAAGAAGGTCGAACTCAAGAGCAATCATCCAGCTATTGTGTATCAAAAGAATGT
TGCTAATCGTTTGAAGCTCTTAGCTGCATCAAAGAAAGCTAGACAAGCTCGCGCTGCTGA
AAAGAAAAAAGCTGCTGCTGGAAAGAAAGCAACAAAAAAGACCGCAGCCAAGAAAAAGTA
A

>g3343.t40 Gene=g3343 Length=145
MRRNARQAYAVSAEAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFA
PTKPWRRWHRRINVNLKRYAVVSAVAASGVPALVQARGHIIDGIAELPLVVSDKVQEYNK
TKQAVLFLRRNKFEKGLQSATSNYV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3343.t40 Gene3D G3DSA:3.40.1370.10 - 1 144 1.2E-59
2 g3343.t40 PANTHER PTHR19431 60S RIBOSOMAL PROTEIN L4 1 133 1.2E-70
3 g3343.t40 PANTHER PTHR19431:SF0 60S RIBOSOMAL PROTEIN L4 1 133 1.2E-70
1 g3343.t40 Pfam PF00573 Ribosomal protein L4/L1 family 2 133 4.2E-16
5 g3343.t40 ProSitePatterns PS00939 Ribosomal protein L1e signature. 73 99 -
4 g3343.t40 SUPERFAMILY SSF52166 Ribosomal protein L4 2 142 9.55E-42

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