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.t9 TTS g3343.t9 24752884 24752884
chr_3 g3343 g3343.t9 isoform g3343.t9 24752889 24754257
chr_3 g3343 g3343.t9 exon g3343.t9.exon1 24752889 24753036
chr_3 g3343 g3343.t9 cds g3343.t9.CDS1 24752973 24753036
chr_3 g3343 g3343.t9 exon g3343.t9.exon2 24753165 24753703
chr_3 g3343 g3343.t9 cds g3343.t9.CDS2 24753165 24753703
chr_3 g3343 g3343.t9 exon g3343.t9.exon3 24753929 24754053
chr_3 g3343 g3343.t9 cds g3343.t9.CDS3 24753929 24754053
chr_3 g3343 g3343.t9 exon g3343.t9.exon4 24754107 24754257
chr_3 g3343 g3343.t9 cds g3343.t9.CDS4 24754107 24754245
chr_3 g3343 g3343.t9 TSS g3343.t9 24754851 24754851

Sequences

>g3343.t9 Gene=g3343 Length=963
GCTTTCGGAAATATGTGTCGTGGAGGTCGCATGTTCGCTCCAACTAAACCATGGCGTAGA
TGGCATCGTCGCATTAATGTCAACTTGAAACGTTATGCAGTTGTTTCAGCTGTTGCTGCA
TCAGGCGTTCCAGCTCTTGTTCAAGCTCGAGGACATATTATTGACGGAATTGCTGAACTT
CCATTGGTTGTCTCAGATAAAGTTCAAGAATACAACAAGACCAAACAAGCTGTTTTGTTC
TTACGTCGTAACAAGTTGTGGGGAGATGTTTTGAAAGTTTATCGTTCAAAACGCTTTAGA
GCTGGTCGTGGTAAAATGCGAAATCGTCGTCGTATTCAACGTCGTGGACCATTAATTGTT
TACTCGAAGGATGATGGCTTGCGTCGTGCATTCCGTAATATTCCCGGTGTTGATACAATG
AGCGTTCACAAATTGAATTTGCTCAAATTGGCTCCAGGTGGACATCTTGGACGATTGATT
GTTTGGACCGAAGGCGCTTTCAAGCATTTGAATGCATTGTTTGGAACATGGAGTGAGCCT
TCAACAGTGAAAAAGGCTTACAATCTGCCACATCCAATTATGTCTAACACTGATTTGACT
CGCTTGCTCAAATCACAAGAAATCAAGAGCGTTTTGAATGCACCTAAGAAGAGAGTTTTC
CATCGTGTACGCCGCTTGAATCCATTGAAGAACGCCAGACAAAAGACCAAGTTGAATCCA
TATTCAGAAGTTACTCGTCGTCGTGCATTGTTGGCTAAAGAAAAGCGAAAGTATGAGACA
CAAATTGCCAAGGCAAAGAAGAAGAAGGTCGAACTCAACAAAAAAGACCGCAGCCAAGAA
AAAGTAAATTATAAATTTGATGGTAAATACACATATTAAAGAATTCGAGAAATGTAATCA
TGTTGTACACCATATAATGACGAATTCTGAAAGTTTATAATAAAAATAAAACATGAATCA
AAA

>g3343.t9 Gene=g3343 Length=288
MCRGGRMFAPTKPWRRWHRRINVNLKRYAVVSAVAASGVPALVQARGHIIDGIAELPLVV
SDKVQEYNKTKQAVLFLRRNKLWGDVLKVYRSKRFRAGRGKMRNRRRIQRRGPLIVYSKD
DGLRRAFRNIPGVDTMSVHKLNLLKLAPGGHLGRLIVWTEGAFKHLNALFGTWSEPSTVK
KAYNLPHPIMSNTDLTRLLKSQEIKSVLNAPKKRVFHRVRRLNPLKNARQKTKLNPYSEV
TRRRALLAKEKRKYETQIAKAKKKKVELNKKDRSQEKVNYKFDGKYTY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3343.t9 Coils Coil Coil 244 271 -
7 g3343.t9 Gene3D G3DSA:3.40.1370.10 - 1 210 9.3E-93
3 g3343.t9 PANTHER PTHR19431 60S RIBOSOMAL PROTEIN L4 1 277 3.6E-120
4 g3343.t9 PANTHER PTHR19431:SF0 60S RIBOSOMAL PROTEIN L4 1 277 3.6E-120
1 g3343.t9 Pfam PF00573 Ribosomal protein L4/L1 family 1 167 7.1E-25
2 g3343.t9 Pfam PF14374 60S ribosomal protein L4 C-terminal domain 181 253 7.3E-24
10 g3343.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 45 -
11 g3343.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 28 -
12 g3343.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 29 37 -
13 g3343.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 38 45 -
9 g3343.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 46 288 -
6 g3343.t9 ProSitePatterns PS00939 Ribosomal protein L1e signature. 22 48 -
5 g3343.t9 SUPERFAMILY SSF52166 Ribosomal protein L4 1 167 1.83E-55

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