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.t64 TTS g3343.t64 24752884 24752884
chr_3 g3343 g3343.t64 isoform g3343.t64 24753362 24754747
chr_3 g3343 g3343.t64 exon g3343.t64.exon1 24753362 24753703
chr_3 g3343 g3343.t64 cds g3343.t64.CDS1 24753362 24753703
chr_3 g3343 g3343.t64 exon g3343.t64.exon2 24753929 24754053
chr_3 g3343 g3343.t64 cds g3343.t64.CDS2 24753929 24754053
chr_3 g3343 g3343.t64 exon g3343.t64.exon3 24754107 24754533
chr_3 g3343 g3343.t64 cds g3343.t64.CDS3 24754107 24754533
chr_3 g3343 g3343.t64 exon g3343.t64.exon4 24754639 24754747
chr_3 g3343 g3343.t64 cds g3343.t64.CDS4 24754639 24754650
chr_3 g3343 g3343.t64 TSS g3343.t64 24754851 24754851

Sequences

>g3343.t64 Gene=g3343 Length=1003
AGTTAATTGCATAAAGTTGCGTGTGCATATCGATTTTGTGCAATTACTGAGCGTTTAAAT
TGAAAAAATTAGGAAAAATATTTTTAATAATTTTTGCATGTGGCAAATAAGTAAATCAGC
TGCTCGTCCGCTCGTCAGTGTTTATACTGACAAAAGTGAGGTTATTAAAGATACAACAAT
TCCATTGCCTGCAATTTTCAAGGCTCCAATTCGCCCAGATGTCGTCAATGATGTACATCA
ATTAATGCGTCGTAATGCTCGTCAAGCATACGCTGTTAGCGCTGAAGCAGGCCATCAAAC
ATCAGCTGAATCATGGGGTACAGGTCGTGCTGTTGCTCGTATTCCTCGAGTTCGTGGTGG
TGGTACTCATCGTTCAGGTCAGGGTGCTTTCGGAAATATGTGTCGTGGAGGTCGCATGTT
CGCTCCAACTAAACCATGGCGTAGATGGCATCGTCGCATTAATGTCAACTTGAAACGTTA
TGCAGTTGTTTCAGCTGTTGCTGCATCAGGCGTTCCAGCTCTTGTTCAAGCTCGAGGACA
TATTATTGACGGAATTGCTGAACTTCCATTGGTTGTCTCAGATAAAGTTCAAGAATACAA
CAAGACCAAACAAGCTGTTTTGTTCTTACGTCGTAACAAGTTGTGGGGAGATGTTTTGAA
AGTTTATCGTTCAAAACGCTTTAGAGCTGGTCGTGGTAAAATGCGAAATCGTCGTCGTAT
TCAACGTCGTGGACCATTAATTGTTTACTCGAAGGATGATGGCTTGCGTCGTGCATTCCG
TAATATTCCCGGTGTTGATACAATGAGCGTTCACAAATTGAATTTGCTCAAATTGGCTCC
AGGTGGACATCTTGGACGATTGATTGTTTGGACCGAAGGCGCTTTCAAGCATTTGAATGC
ATTGTTTGGAACATGGAGTGAGCCTTCAACAGTGAAAAAGGCTTACAATCTGCCACATCC
AATTATGTCTAACACTGATTTGACTCGCTTGCTCAAATCACAA

>g3343.t64 Gene=g3343 Length=302
MWQISKSAARPLVSVYTDKSEVIKDTTIPLPAIFKAPIRPDVVNDVHQLMRRNARQAYAV
SAEAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKPWRRWHRR
INVNLKRYAVVSAVAASGVPALVQARGHIIDGIAELPLVVSDKVQEYNKTKQAVLFLRRN
KLWGDVLKVYRSKRFRAGRGKMRNRRRIQRRGPLIVYSKDDGLRRAFRNIPGVDTMSVHK
LNLLKLAPGGHLGRLIVWTEGAFKHLNALFGTWSEPSTVKKAYNLPHPIMSNTDLTRLLK
SQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3343.t64 Gene3D G3DSA:3.40.1370.10 - 7 302 2.5E-131
2 g3343.t64 PANTHER PTHR19431 60S RIBOSOMAL PROTEIN L4 7 301 2.4E-155
3 g3343.t64 PANTHER PTHR19431:SF0 60S RIBOSOMAL PROTEIN L4 7 301 2.4E-155
1 g3343.t64 Pfam PF00573 Ribosomal protein L4/L1 family 28 267 8.4E-40
5 g3343.t64 ProSitePatterns PS00939 Ribosomal protein L1e signature. 122 148 -
4 g3343.t64 SUPERFAMILY SSF52166 Ribosomal protein L4 12 267 1.11E-81

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

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