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.t11 TSS g7488.t11 23981472 23981472
chr_2 g7488 g7488.t11 isoform g7488.t11 23981505 23982843
chr_2 g7488 g7488.t11 exon g7488.t11.exon1 23981505 23981509
chr_2 g7488 g7488.t11 cds g7488.t11.CDS1 23981505 23981509
chr_2 g7488 g7488.t11 exon g7488.t11.exon2 23981890 23981996
chr_2 g7488 g7488.t11 cds g7488.t11.CDS2 23981890 23981996
chr_2 g7488 g7488.t11 exon g7488.t11.exon3 23982238 23982423
chr_2 g7488 g7488.t11 cds g7488.t11.CDS3 23982238 23982423
chr_2 g7488 g7488.t11 exon g7488.t11.exon4 23982478 23982843
chr_2 g7488 g7488.t11 cds g7488.t11.CDS4 23982478 23982725
chr_2 g7488 g7488.t11 TTS g7488.t11 23982841 23982841

Sequences

>g7488.t11 Gene=g7488 Length=664
ATGAGTTCCCTCAAGTTGCAGAAGAGGCTTGCAGCCTCAGTAATGAAATGTGGCAAGAAG
AAGGTGTGGTTGGATCCAAATGAAACTAATGAAATCGGCAATACAAATTCTCGTCAAAAT
ATTCGCAAATTGATTAAGGATGGTCTCATCATCAAGAAGCCAGTCGTCGTCCACAGTAGA
TTCCGCGTTCGCAAAAATACCATTGCTCGTCGTAAGGGACGTCACTGTGGTTATGGAAAG
CGTAAAGGTACAGCTAATGCGAGAATGCCTCAAAAATTCCTATGGATGACTCGCATGCAT
CTGTATCACGATTTGTACATGAAATCAAAAGGTAATGTTTTCAAAAATAAGCGCGTTCTT
ATGGAGCACATTCACAAGCGTAAAGCAGAAAAGGCTCGTACAAAGATGTTGAACGATCAA
GCTGAAGCACGCAGAAACAGAGTCCGTGAAGCAAGAAAACGTCGCGAACAGAGAATCGCA
AATAAGAAGCAAGAATTATTGCAGACTTATGCAAAGGAGGAAGAAACTCCAGCCGCTAAG
AAATAAATTATGCGATATTTTAAGAACCTAACGCAAATTTCATAATGAAAAAATTTCCAT
CTGATGTGTGAAAGTAATAAAAGAATTTTTCAAATAAAATTTACTGAAAAATATCTAAAA
TCAA

>g7488.t11 Gene=g7488 Length=181
MSSLKLQKRLAASVMKCGKKKVWLDPNETNEIGNTNSRQNIRKLIKDGLIIKKPVVVHSR
FRVRKNTIARRKGRHCGYGKRKGTANARMPQKFLWMTRMHLYHDLYMKSKGNVFKNKRVL
MEHIHKRKAEKARTKMLNDQAEARRNRVREARKRREQRIANKKQELLQTYAKEEETPAAK
K

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g7488.t11 CDD cd01417 Ribosomal_L19e_E 4 149 2.16608E-72
9 g7488.t11 Coils Coil Coil 138 165 -
6 g7488.t11 Gene3D G3DSA:1.10.1650.10 - 1 56 1.0E-32
8 g7488.t11 Gene3D G3DSA:1.10.1200.240 - 57 100 3.6E-18
7 g7488.t11 Gene3D G3DSA:1.10.1200.240 - 101 178 4.8E-29
13 g7488.t11 MobiDBLite mobidb-lite consensus disorder prediction 131 157 -
3 g7488.t11 PANTHER PTHR10722:SF30 RIBOSOMAL PROTEIN L19 1 176 4.2E-77
4 g7488.t11 PANTHER PTHR10722 60S RIBOSOMAL PROTEIN L19 1 176 4.2E-77
2 g7488.t11 Pfam PF01280 Ribosomal protein L19e 4 99 2.3E-40
1 g7488.t11 Pfam PF01280 Ribosomal protein L19e 100 128 3.8E-7
11 g7488.t11 ProSitePatterns PS00526 Ribosomal protein L19e signature. 7 26 -
12 g7488.t11 SMART SM01416 Ribosomal_L19e_2 3 128 4.9E-73
5 g7488.t11 SUPERFAMILY SSF48140 Ribosomal protein L19 (L19e) 3 126 3.79E-53

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

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. There were no conditions that were differentially expressed