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.t2 isoform g11262.t2 15146044 15155117
chr_1 g11262 g11262.t2 exon g11262.t2.exon1 15146044 15146050
chr_1 g11262 g11262.t2 exon g11262.t2.exon2 15154157 15154737
chr_1 g11262 g11262.t2 cds g11262.t2.CDS1 15154210 15154737
chr_1 g11262 g11262.t2 exon g11262.t2.exon3 15154802 15154893
chr_1 g11262 g11262.t2 cds g11262.t2.CDS2 15154802 15154893
chr_1 g11262 g11262.t2 exon g11262.t2.exon4 15154952 15155023
chr_1 g11262 g11262.t2 cds g11262.t2.CDS3 15154952 15155023
chr_1 g11262 g11262.t2 exon g11262.t2.exon5 15155090 15155117
chr_1 g11262 g11262.t2 cds g11262.t2.CDS4 15155090 15155117
chr_1 g11262 g11262.t2 TSS g11262.t2 15155148 15155148
chr_1 g11262 g11262.t2 TTS g11262.t2 NA NA

Sequences

>g11262.t2 Gene=g11262 Length=780
ATGTTGTGCTCAAGAACAAATTTGTTTTCAAATTTAACATCTATTAGATTAGTTCCTGCT
GCATTTCTCAAAAATTTTCCACCTCCACCAACTTATGATCATGTTGAATTTGGAGAAGGT
AAACCAAAACTTCGATTTTTTGATAAAGTACCCCAATATCCACCAAATATGCGTCCTCCA
AAAATGCAAAAAAAATTGAAATTCATGAGAGGACCTGAGCAAGTTCACAATTTTCTTTTG
CATGAACAATATGGCATTCAAGCATTAGGTGGTGGTAGAATGAGATGGGGTCATTTTGAA
ATGATTCGTTTGAGTGTAGGTCGTAAAATGGATGTGAATAGAATGTTCTGTATTTGGAGA
ATTGATCCACCATGGCAACCAGTGACTAGAAGAGGTCAAGGTCAACGTTTAGGAGGTGGA
AAAGGTGCTATTGATCATTATGTGACACCAATTAAAGCAGGAAGAATTATTATGGAATTA
GGAGGAAAATGTGAATTTAAAGAAGTGCAAGAATTTCTTCAAAAATATGCAGATCAATTG
CCTTTCCCTGCACGAGCTGTCTCTCATGAAATGCTAATAAATGAGAAAAAACATCAAGAA
GAACTTGAAAAATCAAATCTTAATCCATACACATTCAAATATATAATTCAGAATAATTTG
AGTGGCTGTCATAGATGGTTAAGACCAATAGATCATAAGCAATTTGGAAAGTTTGAATAG
AATGACATATTAATAAAAATCAAAATATTAGTAGACATCATGACGCAATTTTACACACAT

>g11262.t2 Gene=g11262 Length=239
MLCSRTNLFSNLTSIRLVPAAFLKNFPPPPTYDHVEFGEGKPKLRFFDKVPQYPPNMRPP
KMQKKLKFMRGPEQVHNFLLHEQYGIQALGGGRMRWGHFEMIRLSVGRKMDVNRMFCIWR
IDPPWQPVTRRGQGQRLGGGKGAIDHYVTPIKAGRIIMELGGKCEFKEVQEFLQKYADQL
PFPARAVSHEMLINEKKHQEELEKSNLNPYTFKYIIQNNLSGCHRWLRPIDHKQFGKFE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11262.t2 CDD cd01433 Ribosomal_L16_L10e 83 187 6.40351E-19
9 g11262.t2 Gene3D G3DSA:3.90.1170.10 - 52 238 2.6E-43
2 g11262.t2 PANTHER PTHR12220:SF13 39S RIBOSOMAL PROTEIN L16, MITOCHONDRIAL 56 190 1.5E-32
3 g11262.t2 PANTHER PTHR12220 50S/60S RIBOSOMAL PROTEIN L16 56 190 1.5E-32
6 g11262.t2 PRINTS PR00060 Ribosomal protein L16 signature 76 88 3.7E-5
4 g11262.t2 PRINTS PR00060 Ribosomal protein L16 signature 112 141 3.7E-5
5 g11262.t2 PRINTS PR00060 Ribosomal protein L16 signature 142 171 3.7E-5
1 g11262.t2 Pfam PF00252 Ribosomal protein L16p/L10e 60 187 6.8E-29
7 g11262.t2 SUPERFAMILY SSF54686 Ribosomal protein L16p/L10e 52 190 5.89E-33
8 g11262.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 20 -

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

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