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.t28 TTS g3343.t28 24752884 24752884
chr_3 g3343 g3343.t28 isoform g3343.t28 24753005 24754269
chr_3 g3343 g3343.t28 exon g3343.t28.exon1 24753005 24753432
chr_3 g3343 g3343.t28 cds g3343.t28.CDS1 24753393 24753432
chr_3 g3343 g3343.t28 exon g3343.t28.exon2 24753510 24753703
chr_3 g3343 g3343.t28 cds g3343.t28.CDS2 24753510 24753703
chr_3 g3343 g3343.t28 exon g3343.t28.exon3 24753929 24754053
chr_3 g3343 g3343.t28 cds g3343.t28.CDS3 24753929 24754053
chr_3 g3343 g3343.t28 exon g3343.t28.exon4 24754107 24754269
chr_3 g3343 g3343.t28 cds g3343.t28.CDS4 24754107 24754245
chr_3 g3343 g3343.t28 TSS g3343.t28 24754851 24754851

Sequences

>g3343.t28 Gene=g3343 Length=910
TCAGGTCAGGGTGCTTTCGGAAATATGTGTCGTGGAGGTCGCATGTTCGCTCCAACTAAA
CCATGGCGTAGATGGCATCGTCGCATTAATGTCAACTTGAAACGTTATGCAGTTGTTTCA
GCTGTTGCTGCATCAGGCGTTCCAGCTCTTGTTCAAGCTCGAGGACATATTATTGACGGA
ATTGCTGAACTTCCATTGGTTGTCTCAGATAAAGTTCAAGAATACAACAAGACCAAACAA
GCTGTTTTGTTCTTACGTCGTAACAAGTTGTGGGGAGATGTTTTGAAAGTTTATCGTTCA
AAACGCTTTAGAGCTGGTCGTGGTAAAATGCGAAATCGTCGTCGTATTCAACGTCGTGGA
CCATTAATTGTTTACTCGAAGGATGATGGCTTGCGTCGTGCATTCCGTAATATTCCCGGT
GTTGATACAATGAGCGTTCACAAATTGAATTTGCTCAAATTGGCTCCAGGTGGACATCTT
GGTGAAAAAGGCTTACAATCTGCCACATCCAATTATGTCTAACACTGATTTGACTCGCTT
GCTCAAATCACAAGAAATCAAGAGCGTTTTGAATGCACCTAAGAAGAGAGTTTTCCATCG
TGTACGCCGCTTGAATCCATTGAAGAACGCCAGACAAAAGACCAAGTTGAATCCATATTC
AGAAGTTACTCGTCGTCGTGCATTGTTGGCTAAAGAAAAGCGAAAGTATGAGACACAAAT
TGCCAAGGCAAAGAAGAAGAAGGTCGAACTCAAGAGCAATCATCCAGCTATTGTGTATCA
AAAGAATGTTGCTAATCGTTTGAAGCTCTTAGCTGCATCAAAGAAAGCTAGACAAGCTCG
CGCTGCTGAAAAGAAAAAAGCTGCTGCTGGAAAGAAAGCAACAAAAAAGACCGCAGCCAA
GAAAAAGTAA

>g3343.t28 Gene=g3343 Length=165
MCRGGRMFAPTKPWRRWHRRINVNLKRYAVVSAVAASGVPALVQARGHIIDGIAELPLVV
SDKVQEYNKTKQAVLFLRRNKLWGDVLKVYRSKRFRAGRGKMRNRRRIQRRGPLIVYSKD
DGLRRAFRNIPGVDTMSVHKLNLLKLAPGGHLGEKGLQSATSNYV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3343.t28 Gene3D G3DSA:3.40.1370.10 - 1 159 2.3E-69
2 g3343.t28 PANTHER PTHR19431 60S RIBOSOMAL PROTEIN L4 1 154 2.4E-80
3 g3343.t28 PANTHER PTHR19431:SF0 60S RIBOSOMAL PROTEIN L4 1 154 2.4E-80
1 g3343.t28 Pfam PF00573 Ribosomal protein L4/L1 family 1 152 7.3E-22
8 g3343.t28 Phobius SIGNAL_PEPTIDE Signal peptide region 1 45 -
9 g3343.t28 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 28 -
10 g3343.t28 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 29 37 -
11 g3343.t28 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 38 45 -
7 g3343.t28 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 46 165 -
5 g3343.t28 ProSitePatterns PS00939 Ribosomal protein L1e signature. 22 48 -
4 g3343.t28 SUPERFAMILY SSF52166 Ribosomal protein L4 1 153 1.18E-48

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