General information for g11012.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L19, mitochondrial.
Parent gene
- The parent gene g11012 is located on chr_1: 13396505..13397722 (+ strand)
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.t16 | TSS | g11012.t16 | 13395385 | 13395385 |
| chr_1 | g11012 | g11012.t16 | isoform | g11012.t16 | 13395410 | 13396505 |
| chr_1 | g11012 | g11012.t16 | exon | g11012.t16.exon1 | 13395410 | 13395740 |
| chr_1 | g11012 | g11012.t16 | exon | g11012.t16.exon2 | 13395806 | 13396505 |
| chr_1 | g11012 | g11012.t16 | cds | g11012.t16.CDS1 | 13395834 | 13396505 |
| chr_1 | g11012 | g11012.t16 | TTS | g11012.t16 | 13396556 | 13396556 |
Sequences
>g11012.t16 Gene=g11012 Length=1031
ATGTTGAGAATATTACCGAAAAATTCTAATTACTTTGTTAATTCACAATGTAAGTTTATG
ACAATAATTTAAAAGTAATGATAATTCTTAAAAGTAAAAGTTGTTGATATTTGTATTAAA
TAAATTTTAGTAATTTTAAGTGAAATTTTAAATTTTATTCTTTAGTTTTATTCTTAAGAC
ATTCATCGTCCGCTCCAGCAGCAGCAACTAATGAAAAAAACAAGGAAATTGCCAATTATG
CTGATAAAAAGAGAATAAAAAAGGGTTCAAAGAAGATCCCAAACGATTTTAGATTCAAAT
ATCAAGATTTTCTTCCAAGTCCAACTGCAAGATACAGAAATAGCTTGTTGGAAAAATTAA
TGAGAAAAGATATGCTTGAAAGAAGGTCACAAGTTCATATTCCCGAATTTTATGTTGGTT
CTATACTGAAAGTGACAATTTCTGATCCTCATTCACAAGGAAAAACAAACAGTTTTGTTG
GTATATGCACTCAAAGAGAATACACTGGATTATGCACAAGAATAACACTGCGAAATGTTA
TTGATCATCAAGGCATTGATGTTGCATATGATATTTATGATCCTCTCATTCAAAAAATTG
AAGTGTTGAAACTAGAGAAGCGACTGGATGATAGAATGCTTTATTTGAGAGATGCATTGC
CTGAATACAGCACAGTAGATGTTAATATGGAACCTGAACTTTTAGCTGAAGGAGCGCCAG
TACCAGTAAATGAAACGATTGTCAAAATGAAACCGTTACCTTGGATGCAAAAATGGGAAA
GAAAAGAATTAAAAGGAATTGAAAATCTTGACCAATATCTTAACCTTTGGAGAAAACAAC
AAAGAGAAAAACAGGCAACTCCATGGGAAAAGTATGATTTGATGAAAGAGTATCGTAGAA
CGATTCCAGAAGAACAGCAGAATAAAATTTTCAGTGAAATATTCGATCGAATTAATAAGA
TAAATGAAGAGCATAAGATAAAAGCAAAAGCAGCCAGAAGAACCATCACTAAGCCACAAA
ATATTCGATAA
>g11012.t16 Gene=g11012 Length=223
MRKDMLERRSQVHIPEFYVGSILKVTISDPHSQGKTNSFVGICTQREYTGLCTRITLRNV
IDHQGIDVAYDIYDPLIQKIEVLKLEKRLDDRMLYLRDALPEYSTVDVNMEPELLAEGAP
VPVNETIVKMKPLPWMQKWERKELKGIENLDQYLNLWRKQQREKQATPWEKYDLMKEYRR
TIPEEQQNKIFSEIFDRINKINEEHKIKAKAARRTITKPQNIR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11012.t16 | Gene3D | G3DSA:2.30.30.790 | - | 1 | 113 | 0.0e+00 |
| 2 | g11012.t16 | PANTHER | PTHR15680:SF9 | 39S RIBOSOMAL PROTEIN L19, MITOCHONDRIAL | 2 | 133 | 0.0e+00 |
| 3 | g11012.t16 | PANTHER | PTHR15680 | RIBOSOMAL PROTEIN L19 | 2 | 133 | 0.0e+00 |
| 5 | g11012.t16 | PRINTS | PR00061 | Ribosomal protein L19 signature | 1 | 27 | 3.6e-06 |
| 6 | g11012.t16 | PRINTS | PR00061 | Ribosomal protein L19 signature | 30 | 59 | 3.6e-06 |
| 4 | g11012.t16 | PRINTS | PR00061 | Ribosomal protein L19 signature | 60 | 83 | 3.6e-06 |
| 1 | g11012.t16 | Pfam | PF01245 | Ribosomal protein L19 | 8 | 99 | 0.0e+00 |
| 7 | g11012.t16 | SUPERFAMILY | SSF50104 | Translation proteins SH3-like domain | 11 | 132 | 0.0e+00 |
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 transcript has been annotated with K02884 (large subunit ribosomal protein L19)
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.
