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.t17 TSS g7488.t17 23981472 23981472
chr_2 g7488 g7488.t17 isoform g7488.t17 23981505 23988070
chr_2 g7488 g7488.t17 exon g7488.t17.exon1 23981505 23981509
chr_2 g7488 g7488.t17 cds g7488.t17.CDS1 23981505 23981509
chr_2 g7488 g7488.t17 exon g7488.t17.exon2 23981890 23981996
chr_2 g7488 g7488.t17 cds g7488.t17.CDS2 23981890 23981996
chr_2 g7488 g7488.t17 exon g7488.t17.exon3 23982238 23982830
chr_2 g7488 g7488.t17 cds g7488.t17.CDS3 23982238 23982725
chr_2 g7488 g7488.t17 TTS g7488.t17 23982841 23982841
chr_2 g7488 g7488.t17 exon g7488.t17.exon4 23988048 23988070

Sequences

>g7488.t17 Gene=g7488 Length=728
ATGAGTTCCCTCAAGTTGCAGAAGAGGCTTGCAGCCTCAGTAATGAAATGTGGCAAGAAG
AAGGTGTGGTTGGATCCAAATGAAACTAATGAAATCGGCAATACAAATTCTCGTCAAAAT
ATTCGCAAATTGATTAAGGATGGTCTCATCATCAAGAAGCCAGTCGTCGTCCACAGTAGA
TTCCGCGTTCGCAAAAATACCATTGCTCGTCGTAAGGGACGTCACTGTGGTTATGGAAAG
CGTAAAGGTACAGCTAATGCGAGAATGCCTCAAAAATTCCTATGGATGACTCGCATGCGT
GTCCTTCGTCGTCTCTTGAAAAAATACCGTGAAGCAAAGAAAATCGATCGTCATCTGTAT
CACGATTTGTACATGAAATCAAAAGGTAATGTTTTCAAAAATAAGCGCGTTCTTATGGAG
CACATTCACAAGCGTAAAGCAGAAAAGGCTCGTACAAAGATGTTGAACGATCAAGCTGAA
GCACGCAGAAACAGAGTCCGTGAAGCAAGAAAACGTCGCGAACAGAGAATCGCAAATAAG
AAGCAAGAATTATTGCAGACTTATGCAAAGGAGGAAGAAACTCCAGCCGCTAAGAAATAA
ATTATGCGATATTTTAAGAACCTAACGCAAATTTCATAATGAAAAAATTTCCATCTGATG
TGTGAAAGTAATAAAAGAATTTTTCAAATAAAATTTACTGAAAAATATAAAATCAAAAAA
TAAACCTT

>g7488.t17 Gene=g7488 Length=199
MSSLKLQKRLAASVMKCGKKKVWLDPNETNEIGNTNSRQNIRKLIKDGLIIKKPVVVHSR
FRVRKNTIARRKGRHCGYGKRKGTANARMPQKFLWMTRMRVLRRLLKKYREAKKIDRHLY
HDLYMKSKGNVFKNKRVLMEHIHKRKAEKARTKMLNDQAEARRNRVREARKRREQRIANK
KQELLQTYAKEEETPAAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7488.t17 CDD cd01417 Ribosomal_L19e_E 4 167 5.50944E-85
8 g7488.t17 Coils Coil Coil 156 183 -
6 g7488.t17 Gene3D G3DSA:1.10.1650.10 - 1 56 1.2E-32
7 g7488.t17 Gene3D G3DSA:1.10.1200.240 - 57 196 2.1E-65
4 g7488.t17 Hamap MF_01475 50S ribosomal protein L19e [rpl19e]. 3 149 20.039391
12 g7488.t17 MobiDBLite mobidb-lite consensus disorder prediction 148 175 -
2 g7488.t17 PANTHER PTHR10722:SF30 RIBOSOMAL PROTEIN L19 1 194 2.9E-94
3 g7488.t17 PANTHER PTHR10722 60S RIBOSOMAL PROTEIN L19 1 194 2.9E-94
1 g7488.t17 Pfam PF01280 Ribosomal protein L19e 4 145 4.7E-63
11 g7488.t17 ProSitePatterns PS00526 Ribosomal protein L19e signature. 7 26 -
10 g7488.t17 SMART SM01416 Ribosomal_L19e_2 3 146 2.3E-96
5 g7488.t17 SUPERFAMILY SSF48140 Ribosomal protein L19 (L19e) 3 144 1.44E-64

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