Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L35a.

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 g9650 g9650.t13 TSS g9650.t13 4478269 4478269
chr_1 g9650 g9650.t13 isoform g9650.t13 4478287 4479303
chr_1 g9650 g9650.t13 exon g9650.t13.exon1 4478287 4478309
chr_1 g9650 g9650.t13 cds g9650.t13.CDS1 4478288 4478309
chr_1 g9650 g9650.t13 exon g9650.t13.exon2 4478748 4478935
chr_1 g9650 g9650.t13 cds g9650.t13.CDS2 4478748 4478935
chr_1 g9650 g9650.t13 exon g9650.t13.exon3 4479105 4479303
chr_1 g9650 g9650.t13 cds g9650.t13.CDS3 4479105 4479302
chr_1 g9650 g9650.t13 TTS g9650.t13 4479425 4479425

Sequences

>g9650.t13 Gene=g9650 Length=410
TTCAATAAAACGTGTGAAAGTGACAGCAAAAAAAGAAAAGAAACCAGCGGCTGAAGCTGC
ACCAGCAAAACCTAAAGCAAAGGCACCAGCAGAACCAAAAGCTGTAACTCCACGACCATT
CAAACGTTATGGTAGATTATGGGCTAAGGCTGTCTTTACTGGTTTCAAGCGTGGCTTGAG
AAATCAACACGAGAATCACGCTCTTCTCAAGATTGAAGGATCACGTAGCCGAAAAACATC
ATTGTTCTATGTTGGTAAACGCTGTGTATTTGTTTACAAAGGTAAATCCAAAAAATCATC
GCCAACAAATCCAAAACACAAGTCTCGTCTGCGAGCAATTTGGGGAAAAGTTACCCGACT
TCACGGTAATAATGGCAGCGTTCGTGCTCGCTTCAAGACAAATTTGCCAG

>g9650.t13 Gene=g9650 Length=136
SIKRVKVTAKKEKKPAAEAAPAKPKAKAPAEPKAVTPRPFKRYGRLWAKAVFTGFKRGLR
NQHENHALLKIEGSRSRKTSLFYVGKRCVFVYKGKSKKSSPTNPKHKSRLRAIWGKVTRL
HGNNGSVRARFKTNLP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g9650.t13 Gene3D G3DSA:2.40.10.190 translation elongation factor selb 43 136 9.6E-38
5 g9650.t13 MobiDBLite mobidb-lite consensus disorder prediction 1 35 -
2 g9650.t13 PANTHER PTHR10902 60S RIBOSOMAL PROTEIN L35A 35 136 7.8E-31
1 g9650.t13 Pfam PF01247 Ribosomal protein L35Ae 46 136 3.1E-33
4 g9650.t13 ProSitePatterns PS01105 Ribosomal protein L35Ae signature. 115 136 -
3 g9650.t13 SUPERFAMILY SSF50447 Translation proteins 46 136 3.41E-27

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