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.t7 TSS g9650.t7 4478269 4478269
chr_1 g9650 g9650.t7 isoform g9650.t7 4478281 4479451
chr_1 g9650 g9650.t7 exon g9650.t7.exon1 4478281 4478297
chr_1 g9650 g9650.t7 exon g9650.t7.exon2 4478711 4478935
chr_1 g9650 g9650.t7 cds g9650.t7.CDS1 4478711 4478935
chr_1 g9650 g9650.t7 exon g9650.t7.exon3 4479105 4479451
chr_1 g9650 g9650.t7 cds g9650.t7.CDS2 4479105 4479356
chr_1 g9650 g9650.t7 TTS g9650.t7 4479425 4479425

Sequences

>g9650.t7 Gene=g9650 Length=589
GGTAATTTCAATAAAACATGGCCGATACAGCAGCAAAAACAAAAGCTGCCCCAGCAGCAA
AAAAAGAAAAGAAACCAGCGGCTGAAGCTGCACCAGCAAAACCTAAAGCAAAGGCACCAG
CAGAACCAAAAGCTGTAACTCCACGACCATTCAAACGTTATGGTAGATTATGGGCTAAGG
CTGTCTTTACTGGTTTCAAGCGTGGCTTGAGAAATCAACACGAGAATCACGCTCTTCTCA
AGATTGAAGGATCACGTAGCCGAAAAACATCATTGTTCTATGTTGGTAAACGCTGTGTAT
TTGTTTACAAAGGTAAATCCAAAAAATCATCGCCAACAAATCCAAAACACAAGTCTCGTC
TGCGAGCAATTTGGGGAAAAGTTACCCGACTTCACGGTAATAATGGCAGCGTTCGTGCTC
GCTTCAAGACAAATTTGCCAGGTGATGCAATGGGACATCGTGTAAGAATTATGCTCTATC
CATCAAGAATTTAAATTTAATCTTGTATATTGGATTTGAAGAACATACAACAAACAGAAT
AAAAACCTCCGTTTGAGAATTCCAATTTAAATTTTTTTTTATTTAAAAA

>g9650.t7 Gene=g9650 Length=158
MADTAAKTKAAPAAKKEKKPAAEAAPAKPKAKAPAEPKAVTPRPFKRYGRLWAKAVFTGF
KRGLRNQHENHALLKIEGSRSRKTSLFYVGKRCVFVYKGKSKKSSPTNPKHKSRLRAIWG
KVTRLHGNNGSVRARFKTNLPGDAMGHRVRIMLYPSRI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g9650.t7 Gene3D G3DSA:2.40.10.190 translation elongation factor selb 48 158 8.8E-48
3 g9650.t7 Hamap MF_00573 50S ribosomal protein L35Ae [rpl35ae]. 53 152 24.194084
6 g9650.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 42 -
7 g9650.t7 MobiDBLite mobidb-lite consensus disorder prediction 10 25 -
2 g9650.t7 PANTHER PTHR10902 60S RIBOSOMAL PROTEIN L35A 44 158 4.1E-39
1 g9650.t7 Pfam PF01247 Ribosomal protein L35Ae 51 152 8.8E-39
5 g9650.t7 ProSitePatterns PS01105 Ribosomal protein L35Ae signature. 120 141 -
4 g9650.t7 SUPERFAMILY SSF50447 Translation proteins 51 152 2.0E-32

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

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