Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 39S ribosomal protein L16, 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 g11262 g11262.t4 isoform g11262.t4 15146044 15155117
chr_1 g11262 g11262.t4 exon g11262.t4.exon1 15146044 15146050
chr_1 g11262 g11262.t4 exon g11262.t4.exon2 15154155 15155117
chr_1 g11262 g11262.t4 cds g11262.t4.CDS1 15154210 15154725
chr_1 g11262 g11262.t4 TSS g11262.t4 15155148 15155148
chr_1 g11262 g11262.t4 TTS g11262.t4 NA NA

Sequences

>g11262.t4 Gene=g11262 Length=970
ATGTTGTGCTCAAGAACAAATTTGTTTTGTAAGTGAAATACAAAGAGACACCATATATAA
AATAGTTAATAATCATTGCTTCATTCTTTTATAGCAAATTTAACATCTATTAGATTAGTT
CCTGCTGCATTTCTCAAAAATTTTCCACCTCCACCAACTTATGATCGTAGGTTTATCATA
ATTTGAATTTTAGCATTAAATGACTAATAATTGCTTAATTACAGATGTTGAATTTGGAGA
AGGTAAACCAAAACTTCGATTTTTTGATAAAGTACCCCAATATCCACCAAATATGCGTCC
TCCAAAAATGCAAAAAGTAAGTTGCACAATGAGTTGATCCAGTAGAGTAAAATTAATTTA
TAAAATCTTTCATTTTTCAGAAATTGAAATTCATGAGAGGACCTGAGCAAGTTCACAATT
TTCTTTTGCATGAACAATATGGCATTCAAGCATTAGGTGGTGGTAGAATGAGATGGGGTC
ATTTTGAAATGATTCGTTTGAGTGTAGGTCGTAAAATGGATGTGAATAGAATGTTCTGTA
TTTGGAGAATTGATCCACCATGGCAACCAGTGACTAGAAGAGGTCAAGGTCAACGTTTAG
GAGGTGGAAAAGGTGCTATTGATCATTATGTGACACCAATTAAAGCAGGAAGAATTATTA
TGGAATTAGGAGGAAAATGTGAATTTAAAGAAGTGCAAGAATTTCTTCAAAAATATGCAG
ATCAATTGCCTTTCCCTGCACGAGCTGTCTCTCATGAAATGCTAATAAATGAGAAAAAAC
ATCAAGAAGAACTTGAAAAATCAAATCTTAATCCATACACATTCAAATATATAATTCAGA
ATAATTTGAGTGGCTGTCATAGATGGTTAAGACCAATAGATCATAAGCAATTTGGAAAGT
TTGAATAGAATGACATATTAATAAAAATCAAAATATTAGTAGACATCATGACGCAATTTT
AAACACACAT

>g11262.t4 Gene=g11262 Length=171
MRGPEQVHNFLLHEQYGIQALGGGRMRWGHFEMIRLSVGRKMDVNRMFCIWRIDPPWQPV
TRRGQGQRLGGGKGAIDHYVTPIKAGRIIMELGGKCEFKEVQEFLQKYADQLPFPARAVS
HEMLINEKKHQEELEKSNLNPYTFKYIIQNNLSGCHRWLRPIDHKQFGKFE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11262.t4 CDD cd01433 Ribosomal_L16_L10e 15 119 0.0e+00
8 g11262.t4 Gene3D G3DSA:3.90.1170.10 - 1 170 0.0e+00
2 g11262.t4 PANTHER PTHR12220:SF13 39S RIBOSOMAL PROTEIN L16, MITOCHONDRIAL 1 122 0.0e+00
3 g11262.t4 PANTHER PTHR12220 50S/60S RIBOSOMAL PROTEIN L16 1 122 0.0e+00
4 g11262.t4 PRINTS PR00060 Ribosomal protein L16 signature 8 20 1.8e-05
5 g11262.t4 PRINTS PR00060 Ribosomal protein L16 signature 44 73 1.8e-05
6 g11262.t4 PRINTS PR00060 Ribosomal protein L16 signature 74 103 1.8e-05
1 g11262.t4 Pfam PF00252 Ribosomal protein L16p/L10e 2 119 0.0e+00
7 g11262.t4 SUPERFAMILY SSF54686 Ribosomal protein L16p/L10e 1 123 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
GO:0019843 rRNA binding 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