Gene loci information

Transcript annotation

  • This transcript has been annotated as 39S ribosomal protein L19, mitochondrial.

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_1 g11012 g11012.t15 TSS g11012.t15 13395385 13395385
chr_1 g11012 g11012.t15 isoform g11012.t15 13395410 13396505
chr_1 g11012 g11012.t15 exon g11012.t15.exon1 13395410 13395458
chr_1 g11012 g11012.t15 cds g11012.t15.CDS1 13395410 13395458
chr_1 g11012 g11012.t15 exon g11012.t15.exon2 13395575 13395740
chr_1 g11012 g11012.t15 cds g11012.t15.CDS2 13395575 13395740
chr_1 g11012 g11012.t15 exon g11012.t15.exon3 13395806 13396267
chr_1 g11012 g11012.t15 cds g11012.t15.CDS3 13395806 13396267
chr_1 g11012 g11012.t15 exon g11012.t15.exon4 13396384 13396505
chr_1 g11012 g11012.t15 cds g11012.t15.CDS4 13396384 13396399
chr_1 g11012 g11012.t15 TTS g11012.t15 13396556 13396556

Sequences

>g11012.t15 Gene=g11012 Length=799
ATGTTGAGAATATTACCGAAAAATTCTAATTACTTTGTTAATTCACAATTTTTATTCTTA
AGACATTCATCGTCCGCTCCAGCAGCAGCAACTAATGAAAAAAACAAGGAAATTGCCAAT
TATGCTGATAAAAAGAGAATAAAAAAGGGTTCAAAGAAGATCCCAAACGATTTTAGATTC
AAATATCAAGATTTTCTTCCAAGTCCAACTGCAAGATACAGAAATAGCTTGTTGGAAAAA
TTAATGAGAAAAGATATGCTTGAAAGAAGGTCACAAGTTCATATTCCCGAATTTTATGTT
GGTTCTATACTGAAAGTGACAATTTCTGATCCTCATTCACAAGGAAAAACAAACAGTTTT
GTTGGTATATGCACTCAAAGAGAATACACTGGATTATGCACAAGAATAACACTGCGAAAT
GTTATTGATCATCAAGGCATTGATGTTGCATATGATATTTATGATCCTCTCATTCAAAAA
ATTGAAGTGTTGAAACTAGAGAAGCGACTGGATGATAGAATGCTTTATTTGAGAGATGCA
TTGCCTGAATACAGCACAGTAGATGTTAATATGGAACCTGAACTTTTAGCTGAAGGAGCG
CCAGTACCAGTAAATGAAACGATTGTCAAAATGAAACCGTTACCTTGGATGCAAAAATGG
GAAAGAAAAGAATTAAAAAGAACAGCAGAATAAAATTTTCAGTGAAATATTCGATCGAAT
TAATAAGATAAATGAAGAGCATAAGATAAAAGCAAAAGCAGCCAGAAGAACCATCACTAA
GCCACAAAATATTCGATAA

>g11012.t15 Gene=g11012 Length=230
MLRILPKNSNYFVNSQFLFLRHSSSAPAAATNEKNKEIANYADKKRIKKGSKKIPNDFRF
KYQDFLPSPTARYRNSLLEKLMRKDMLERRSQVHIPEFYVGSILKVTISDPHSQGKTNSF
VGICTQREYTGLCTRITLRNVIDHQGIDVAYDIYDPLIQKIEVLKLEKRLDDRMLYLRDA
LPEYSTVDVNMEPELLAEGAPVPVNETIVKMKPLPWMQKWERKELKRTAE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11012.t15 Gene3D G3DSA:2.30.30.790 - 70 193 1.6E-14
2 g11012.t15 PANTHER PTHR15680:SF9 39S RIBOSOMAL PROTEIN L19, MITOCHONDRIAL 22 193 3.3E-37
3 g11012.t15 PANTHER PTHR15680 RIBOSOMAL PROTEIN L19 22 193 3.3E-37
1 g11012.t15 Pfam PF01245 Ribosomal protein L19 89 180 4.6E-13
4 g11012.t15 SUPERFAMILY SSF50104 Translation proteins SH3-like domain 75 213 7.42E-32
5 g11012.t15 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 28 -

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: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