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.t5 TSS g7488.t5 23981472 23981472
chr_2 g7488 g7488.t5 isoform g7488.t5 23981505 23982725
chr_2 g7488 g7488.t5 exon g7488.t5.exon1 23981505 23981509
chr_2 g7488 g7488.t5 exon g7488.t5.exon2 23981900 23982000
chr_2 g7488 g7488.t5 cds g7488.t5.CDS1 23981964 23982000
chr_2 g7488 g7488.t5 exon g7488.t5.exon3 23982238 23982725
chr_2 g7488 g7488.t5 cds g7488.t5.CDS2 23982238 23982725
chr_2 g7488 g7488.t5 TTS g7488.t5 23982841 23982841

Sequences

>g7488.t5 Gene=g7488 Length=594
ATGAGTTGCAGAAGAGGCTTGCAGCCTCAGTAATGAAATGTGGCAAGAAGAAGGTGTGGT
TGGATCCAAATGAAACTAATGAAATCGGCAATACAAATTCTCGTAAGTCAAAATATTCGC
AAATTGATTAAGGATGGTCTCATCATCAAGAAGCCAGTCGTCGTCCACAGTAGATTCCGC
GTTCGCAAAAATACCATTGCTCGTCGTAAGGGACGTCACTGTGGTTATGGAAAGCGTAAA
GGTACAGCTAATGCGAGAATGCCTCAAAAATTCCTATGGATGACTCGCATGCGTGTCCTT
CGTCGTCTCTTGAAAAAATACCGTGAAGCAAAGAAAATCGATCGTCATCTGTATCACGAT
TTGTACATGAAATCAAAAGGTAATGTTTTCAAAAATAAGCGCGTTCTTATGGAGCACATT
CACAAGCGTAAAGCAGAAAAGGCTCGTACAAAGATGTTGAACGATCAAGCTGAAGCACGC
AGAAACAGAGTCCGTGAAGCAAGAAAACGTCGCGAACAGAGAATCGCAAATAAGAAGCAA
GAATTATTGCAGACTTATGCAAAGGAGGAAGAAACTCCAGCCGCTAAGAAATAA

>g7488.t5 Gene=g7488 Length=174
MKLMKSAIQILVSQNIRKLIKDGLIIKKPVVVHSRFRVRKNTIARRKGRHCGYGKRKGTA
NARMPQKFLWMTRMRVLRRLLKKYREAKKIDRHLYHDLYMKSKGNVFKNKRVLMEHIHKR
KAEKARTKMLNDQAEARRNRVREARKRREQRIANKKQELLQTYAKEEETPAAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7488.t5 Coils Coil Coil 131 158 -
7 g7488.t5 Gene3D G3DSA:1.10.1650.10 - 4 31 2.0E-5
8 g7488.t5 Gene3D G3DSA:1.10.1200.240 - 32 171 1.4E-65
6 g7488.t5 MobiDBLite mobidb-lite consensus disorder prediction 123 174 -
2 g7488.t5 PANTHER PTHR10722:SF30 RIBOSOMAL PROTEIN L19 13 169 6.8E-71
3 g7488.t5 PANTHER PTHR10722 60S RIBOSOMAL PROTEIN L19 13 169 6.8E-71
1 g7488.t5 Pfam PF01280 Ribosomal protein L19e 13 121 4.1E-45
5 g7488.t5 SMART SM01416 Ribosomal_L19e_2 4 121 1.8E-53
4 g7488.t5 SUPERFAMILY SSF48140 Ribosomal protein L19 (L19e) 13 119 2.35E-45

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. There were no conditions that were differentially expressed