Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t6 TSS g7488.t6 23981472 23981472
chr_2 g7488 g7488.t6 isoform g7488.t6 23981505 23982725
chr_2 g7488 g7488.t6 exon g7488.t6.exon1 23981505 23981509
chr_2 g7488 g7488.t6 exon g7488.t6.exon2 23981890 23981923
chr_2 g7488 g7488.t6 exon g7488.t6.exon3 23982238 23982725
chr_2 g7488 g7488.t6 cds g7488.t6.CDS1 23982390 23982725
chr_2 g7488 g7488.t6 TTS g7488.t6 23982841 23982841

Sequences

>g7488.t6 Gene=g7488 Length=527
ATGAGTTCCCTCAAGTTGCAGAAGAGGCTTGCAGCCTCAGTCAAAATATTCGCAAATTGA
TTAAGGATGGTCTCATCATCAAGAAGCCAGTCGTCGTCCACAGTAGATTCCGCGTTCGCA
AAAATACCATTGCTCGTCGTAAGGGACGTCACTGTGGTTATGGAAAGCGTAAAGGTACAG
CTAATGCGAGAATGCCTCAAAAATTCCTATGGATGACTCGCATGCGTGTCCTTCGTCGTC
TCTTGAAAAAATACCGTGAAGCAAAGAAAATCGATCGTCATCTGTATCACGATTTGTACA
TGAAATCAAAAGGTAATGTTTTCAAAAATAAGCGCGTTCTTATGGAGCACATTCACAAGC
GTAAAGCAGAAAAGGCTCGTACAAAGATGTTGAACGATCAAGCTGAAGCACGCAGAAACA
GAGTCCGTGAAGCAAGAAAACGTCGCGAACAGAGAATCGCAAATAAGAAGCAAGAATTAT
TGCAGACTTATGCAAAGGAGGAAGAAACTCCAGCCGCTAAGAAATAA

>g7488.t6 Gene=g7488 Length=111
MPQKFLWMTRMRVLRRLLKKYREAKKIDRHLYHDLYMKSKGNVFKNKRVLMEHIHKRKAE
KARTKMLNDQAEARRNRVREARKRREQRIANKKQELLQTYAKEEETPAAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7488.t6 Coils Coil Coil 68 95 -
7 g7488.t6 Gene3D G3DSA:1.10.1200.240 - 1 108 5.6E-47
6 g7488.t6 MobiDBLite mobidb-lite consensus disorder prediction 60 87 -
2 g7488.t6 PANTHER PTHR10722:SF30 RIBOSOMAL PROTEIN L19 1 106 5.4E-42
3 g7488.t6 PANTHER PTHR10722 60S RIBOSOMAL PROTEIN L19 1 106 5.4E-42
1 g7488.t6 Pfam PF01280 Ribosomal protein L19e 1 58 1.5E-21
5 g7488.t6 SMART SM01416 Ribosomal_L19e_2 1 58 3.7E-9
4 g7488.t6 SUPERFAMILY SSF48140 Ribosomal protein L19 (L19e) 1 56 4.18E-21

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.

Raw TPM values