Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 28S ribosomal protein S15, 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_2 g8349 g8349.t4 TSS g8349.t4 29891320 29891320
chr_2 g8349 g8349.t4 isoform g8349.t4 29891351 29892302
chr_2 g8349 g8349.t4 exon g8349.t4.exon1 29891351 29892302
chr_2 g8349 g8349.t4 cds g8349.t4.CDS1 29891799 29892302
chr_2 g8349 g8349.t4 TTS g8349.t4 29892350 29892350

Sequences

>g8349.t4 Gene=g8349 Length=952
ATGCTTAAAAAATTTTCAAAATTACTTTTCTTCAAAAATCAGCTCACTCCATTGCTGATC
ACAGTTAGAAATTATCCTAAGTTTAAAGGAGGAAAACCTGCAATGAAGCATGAAGTTTTT
GATTACATTAAATGGGTACGTCCACAAAAAATTCCAACAATTGATCCTGAAAAAAGTGGC
GATTTAGCTTCAATGCCGAAATATGATTTGAAGCAGTCTTTACTTTATTTTGATAACTCT
TCATTATTGGAAAATGCTAACGAATTAGTCAAGTCAAAATTCACACTAGAACTGAATCCA
GGAAAAGAAGAGAAAGCATTGTATAAAGAGGAGTTAGTGAAGAAAGTTCAGAGACACGAT
CAAGATTATGGCTCAATGGAAGCTAAATGTAAGTTTATAATTAATTAAATTTGAACAATT
ATAATTAATTTCTATTTTAGTGGCAAAAATGACAGCAATCATTCGATATTGGCAAGTTCG
ATTAAAGGAAAATCCTAAAAATTCAAGACTCAAGACGTTAACAAAAGAACTCATTGAGAA
GAGAAAAAAATATTTGAAATTTTTACGTCGAGATGATTACAAGAGGTTTGAATATATACT
CGAACAATTAGAATTGAAATATGTCCCATATCCAAATAAATTTCACTGGATAGCAAGAAA
AGAAGCAATGAGAGCTTTGACAAAAAGATTCTGTCGAGGCATTCAAATTGAAAGATTGAA
AGAATACAAAGCGACACTTCAAGCACAACAGCTTGATTTCTTAGAGAATAAAATCAAAAA
CTTGGAATTCATTAGAAATGAGCAAATTGAATGCAAAGTTCCAGTGACAGTCACAAATGA
AGAAATTAATGCAGTTAAGAAACAATATAAAGAGCTGAAACAGCAGAGAGATGAAGAAGC
TGAAATTCGAAGAAAGAATGAAGTAAGAGACGATTACGAAATTAAATTGTAA

>g8349.t4 Gene=g8349 Length=167
MTAIIRYWQVRLKENPKNSRLKTLTKELIEKRKKYLKFLRRDDYKRFEYILEQLELKYVP
YPNKFHWIARKEAMRALTKRFCRGIQIERLKEYKATLQAQQLDFLENKIKNLEFIRNEQI
ECKVPVTVTNEEINAVKKQYKELKQQRDEEAEIRRKNEVRDDYEIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g8349.t4 Coils Coil Coil 126 156 -
5 g8349.t4 Gene3D G3DSA:1.10.287.10 - 1 57 2.7E-7
2 g8349.t4 PANTHER PTHR46685 28S RIBOSOMAL PROTEIN S15, MITOCHONDRIAL 1 132 1.1E-23
1 g8349.t4 Pfam PF00312 Ribosomal protein S15 1 56 9.4E-8
4 g8349.t4 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 1 57 2.0E-7
3 g8349.t4 SUPERFAMILY SSF50715 Ribosomal protein L25-like 71 136 9.94E-5

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.

Raw TPM values