Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t73 isoform g3343.t73 24754120 24754773
chr_3 g3343 g3343.t73 exon g3343.t73.exon1 24754120 24754533
chr_3 g3343 g3343.t73 cds g3343.t73.CDS1 24754120 24754398
chr_3 g3343 g3343.t73 exon g3343.t73.exon2 24754767 24754773
chr_3 g3343 g3343.t73 TSS g3343.t73 24754851 24754851
chr_3 g3343 g3343.t73 TTS g3343.t73 NA NA

Sequences

>g3343.t73 Gene=g3343 Length=421
ATGGTTAAGTAAATCAGCTGCTCGTCCGCTCGTCAGTGTTTATACTGACAAAAGTGAGGT
TATTAAAGATACAACAATTCCATTGCCTGCAATTTTCAAGGCTCCAATTCGCCCAGATGT
CGTCAATGATGTACATCAATTAATGCGTCGTAATGCTCGTCAAGCATACGCTGTTAGCGC
TGAAGCAGGCCATCAAACATCAGCTGAATCATGGGGTACAGGTCGTGCTGTTGCTCGTAT
TCCTCGAGTTCGTGGTGGTGGTACTCATCGTTCAGGTCAGGGTGCTTTCGGAAATATGTG
TCGTGGAGGTCGCATGTTCGCTCCAACTAAACCATGGCGTAGATGGCATCGTCGCATTAA
TGTCAACTTGAAACGTTATGCAGTTGTTTCAGCTGTTGCTGCATCAGGCGTTCCAGCTCT
T

>g3343.t73 Gene=g3343 Length=93
MRRNARQAYAVSAEAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFA
PTKPWRRWHRRINVNLKRYAVVSAVAASGVPAL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3343.t73 Gene3D G3DSA:3.40.1370.10 - 1 93 2.0E-39
5 g3343.t73 MobiDBLite mobidb-lite consensus disorder prediction 1 28 -
2 g3343.t73 PANTHER PTHR19431 60S RIBOSOMAL PROTEIN L4 3 93 2.7E-50
3 g3343.t73 PANTHER PTHR19431:SF6 BNAC03G35890D PROTEIN 3 93 2.7E-50
1 g3343.t73 Pfam PF00573 Ribosomal protein L4/L1 family 2 88 6.7E-12
4 g3343.t73 SUPERFAMILY SSF52166 Ribosomal protein L4 2 91 9.29E-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: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