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.t18 TTS g3343.t18 24752884 24752884
chr_3 g3343 g3343.t18 isoform g3343.t18 24752889 24754773
chr_3 g3343 g3343.t18 exon g3343.t18.exon1 24752889 24753665
chr_3 g3343 g3343.t18 cds g3343.t18.CDS1 24753005 24753562
chr_3 g3343 g3343.t18 exon g3343.t18.exon2 24754132 24754773
chr_3 g3343 g3343.t18 TSS g3343.t18 24754851 24754851

Sequences

>g3343.t18 Gene=g3343 Length=1419
ATGGTTAGTATTTGTAAATATTCATTAGTTAATTGCATAAAGTTGCGTGTGCATATCGAT
TTTGTGCAATTACTGAGCGTTTAAATTGAAAAAATTAGGAAAAATATTTTTAATAATTTT
TGCATGTGGCAAATAGTAATTTTGACTATTTTCTATTGTTTCCAGCACTAAAATCGTTGC
ACAAACTTAAAGATAAATCATATAAAAATGTATTTTAATTGATATTTCTTTTAATTTTAG
AGTAAATCAGCTGCTCGTCCGCTCGTCAGTGTTTATACTGACAAAAGTGAGGTTATTAAA
GATACAACAATTCCATTGCCTGCAATTTTCAAGGCTCCAATTCGCCCAGATGTCGTCAAT
GATGTACATCAATTAATGCGTCGTAATGCTCGTCAAGCATACGCTGTTAGCGCTGAAGCA
GGCCATCAAACATCAGCTGAATCATGGGGTACAGGTCGTGCTGTTGCTCGTATTCCTCGA
GTTCGTGGTGGTGGTACTCATCGTTCAGGTCAGGGTGCTTTCGGAAATATGTGTCGTGGA
GGTCGCATGTTCGCTCCAACTAAACCATGGCGTAGATGGCATCGTCGCATTAATGTCAAC
TTGAAACGTTATGCAGTTGTTTCAGCTGTTGCTGCATCAGGCAATGCGAAATCGTCGTCG
TATTCAACGTCGTGGACCATTAATTGTTTACTCGAAGGATGATGGCTTGCGTCGTGCATT
CCGTAATATTCCCGGTGTTGATACAATGAGCGTTCACAAATTGAATTTGCTCAAATTGGC
TCCAGGTGGACATCTTGGACGATTGATTGTTTGGACCGAAGGCGCTTTCAAGCATTTGAA
TGCATTGTTTGGAACATGGAGTGAGCCTTCAACAGTGAAAAAGGCTTACAATCTGCCACA
TCCAATTATGTCTAACACTGATTTGACTCGCTTGCTCAAATCACAAGAAATCAAGAGCGT
TTTGAATGCACCTAAGAAGAGAGTTTTCCATCGTGTACGCCGCTTGAATCCATTGAAGAA
CGCCAGACAAAAGACCAAGTTGAATCCATATTCAGAAGTTACTCGTCGTCGTGCATTGTT
GGCTAAAGAAAAGCGAAAGTATGAGACACAAATTGCCAAGGCAAAGAAGAAGAAGGTCGA
ACTCAAGAGCAATCATCCAGCTATTGTGTATCAAAAGAATGTTGCTAATCGTTTGAAGCT
CTTAGCTGCATCAAAGAAAGCTAGACAAGCTCGCGCTGCTGAAAAGAAAAAAGCTGCTGC
TGGAAAGAAAGCAACAAAAAAGACCGCAGCCAAGAAAAAGTAAATTATAAATTTGATGGT
AAATACACATATTAAAGAATTCGAGAAATGTAATCATGTTGTACACCATATAATGACGAA
TTCTGAAAGTTTATAATAAAAATAAAACATGAATCAAAA

>g3343.t18 Gene=g3343 Length=185
MSVHKLNLLKLAPGGHLGRLIVWTEGAFKHLNALFGTWSEPSTVKKAYNLPHPIMSNTDL
TRLLKSQEIKSVLNAPKKRVFHRVRRLNPLKNARQKTKLNPYSEVTRRRALLAKEKRKYE
TQIAKAKKKKVELKSNHPAIVYQKNVANRLKLLAASKKARQARAAEKKKAAAGKKATKKT
AAKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g3343.t18 Coils Coil Coil 109 136 -
6 g3343.t18 Gene3D G3DSA:3.40.1370.10 - 1 74 6.9E-26
5 g3343.t18 MobiDBLite mobidb-lite consensus disorder prediction 157 185 -
2 g3343.t18 PANTHER PTHR19431 60S RIBOSOMAL PROTEIN L4 1 167 4.2E-38
3 g3343.t18 PANTHER PTHR19431:SF0 60S RIBOSOMAL PROTEIN L4 1 167 4.2E-38
1 g3343.t18 Pfam PF14374 60S ribosomal protein L4 C-terminal domain 46 118 3.0E-24
4 g3343.t18 SUPERFAMILY SSF52166 Ribosomal protein L4 2 32 9.16E-7

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