Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L19.

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_2 g7488 g7488.t20 TSS g7488.t20 23981472 23981472
chr_2 g7488 g7488.t20 isoform g7488.t20 23981888 23988070
chr_2 g7488 g7488.t20 exon g7488.t20.exon1 23981888 23981996
chr_2 g7488 g7488.t20 cds g7488.t20.CDS1 23981927 23981996
chr_2 g7488 g7488.t20 exon g7488.t20.exon2 23982238 23982834
chr_2 g7488 g7488.t20 cds g7488.t20.CDS2 23982238 23982725
chr_2 g7488 g7488.t20 TTS g7488.t20 23982841 23982841
chr_2 g7488 g7488.t20 exon g7488.t20.exon3 23988050 23988070

Sequences

>g7488.t20 Gene=g7488 Length=727
AGTTCCCTCAAGTTGCAGAAGAGGCTTGCAGCCTCAGTAATGAAATGTGGCAAGAAGAAG
GTGTGGTTGGATCCAAATGAAACTAATGAAATCGGCAATACAAATTCTCGTCAAAATATT
CGCAAATTGATTAAGGATGGTCTCATCATCAAGAAGCCAGTCGTCGTCCACAGTAGATTC
CGCGTTCGCAAAAATACCATTGCTCGTCGTAAGGGACGTCACTGTGGTTATGGAAAGCGT
AAAGGTACAGCTAATGCGAGAATGCCTCAAAAATTCCTATGGATGACTCGCATGCGTGTC
CTTCGTCGTCTCTTGAAAAAATACCGTGAAGCAAAGAAAATCGATCGTCATCTGTATCAC
GATTTGTACATGAAATCAAAAGGTAATGTTTTCAAAAATAAGCGCGTTCTTATGGAGCAC
ATTCACAAGCGTAAAGCAGAAAAGGCTCGTACAAAGATGTTGAACGATCAAGCTGAAGCA
CGCAGAAACAGAGTCCGTGAAGCAAGAAAACGTCGCGAACAGAGAATCGCAAATAAGAAG
CAAGAATTATTGCAGACTTATGCAAAGGAGGAAGAAACTCCAGCCGCTAAGAAATAAATT
ATGCGATATTTTAAGAACCTAACGCAAATTTCATAATGAAAAAATTTCCATCTGATGTGT
GAAAGTAATAAAAGAATTTTTCAAATAAAATTTACTGAAAAATATCTAAAATCAAAAAAT
AAACCTT

>g7488.t20 Gene=g7488 Length=185
MKCGKKKVWLDPNETNEIGNTNSRQNIRKLIKDGLIIKKPVVVHSRFRVRKNTIARRKGR
HCGYGKRKGTANARMPQKFLWMTRMRVLRRLLKKYREAKKIDRHLYHDLYMKSKGNVFKN
KRVLMEHIHKRKAEKARTKMLNDQAEARRNRVREARKRREQRIANKKQELLQTYAKEEET
PAAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7488.t20 CDD cd01417 Ribosomal_L19e_E 1 153 2.34091E-78
7 g7488.t20 Coils Coil Coil 142 169 -
5 g7488.t20 Gene3D G3DSA:1.10.1650.10 - 1 42 1.1E-23
6 g7488.t20 Gene3D G3DSA:1.10.1200.240 - 43 182 1.7E-65
10 g7488.t20 MobiDBLite mobidb-lite consensus disorder prediction 134 161 -
2 g7488.t20 PANTHER PTHR10722:SF30 RIBOSOMAL PROTEIN L19 1 180 6.4E-87
3 g7488.t20 PANTHER PTHR10722 60S RIBOSOMAL PROTEIN L19 1 180 6.4E-87
1 g7488.t20 Pfam PF01280 Ribosomal protein L19e 1 132 1.6E-56
9 g7488.t20 SMART SM01416 Ribosomal_L19e_2 1 132 6.3E-80
4 g7488.t20 SUPERFAMILY SSF48140 Ribosomal protein L19 (L19e) 1 130 3.27E-58

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:0003723 RNA binding MF
GO:0022625 cytosolic large ribosomal subunit 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