Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L10a.

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_3 g3791 g3791.t40 TTS g3791.t40 27969226 27969226
chr_3 g3791 g3791.t40 isoform g3791.t40 27969305 27970511
chr_3 g3791 g3791.t40 exon g3791.t40.exon1 27969305 27969475
chr_3 g3791 g3791.t40 cds g3791.t40.CDS1 27969305 27969475
chr_3 g3791 g3791.t40 exon g3791.t40.exon2 27969532 27969853
chr_3 g3791 g3791.t40 cds g3791.t40.CDS2 27969532 27969853
chr_3 g3791 g3791.t40 exon g3791.t40.exon3 27970002 27970511
chr_3 g3791 g3791.t40 cds g3791.t40.CDS3 27970002 27970003
chr_3 g3791 g3791.t40 TSS g3791.t40 27970567 27970567

Sequences

>g3791.t40 Gene=g3791 Length=1003
ATGTCGTAAGTTATCCTTATTCAGACATTTTATTATTTTAAAAGTAACAATAAGTAAGCA
GAAAAGTTGAATACATTCAAGTTTTTATTTAAATAACAATATTTTACATAAAAATAATTG
TAATGTTTTAATAACCTAAAATTTCTGCCTATAAGTTGTTACGTTCTGCAGCTATCAAGC
CAAGGATTTAAAGATAATATTACTTTGCTTTCTATGGAAAGGGCTGCAAAATTAATATGG
GTTTTTTCGTATCTTCAATTATCAAAATATATTAAAATAATTGATTACCAAAAAGACCAT
ACATTTTAATCATAAAATTTTATATATTAATACTCTTTCTCTTTGTTTAGATCAAAAGTA
TCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAGTCTCAAGAAAAGAAG
CGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAACTACGATCCACAAAAG
GATAAGCGTTTCAGCGGCACTGTCAAGTATGTTGAAGCACATTCCACGTCCAAAAATGCA
AGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGCAAACGACGTTCCTTT
TATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTTGGTCAAGAAACTCGC
CAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACAAATTCCAAGATTGTT
GGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCAACACAATGAATCAAT
GACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAATGAAGAAGGTCTTGTG
TCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCTCGCTCAAAATGTTCA
CTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCAAAATGTGCGTTCACT
TCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAA

>g3791.t40 Gene=g3791 Length=164
MLKHIPRPKMQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLAS
ESLIKQIPRLLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQMKKVLCLSVAVGHVN
MTPDELAQNVHLSINFMVSLLKKHWQNVRSLHIKSSMGPPQRLY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3791.t40 CDD cd00403 Ribosomal_L1 2 163 1.49583E-47
7 g3791.t40 Gene3D G3DSA:3.30.190.20 - 2 160 2.9E-52
6 g3791.t40 Gene3D G3DSA:3.40.50.790 - 10 100 2.9E-52
2 g3791.t40 PANTHER PTHR23105:SF154 60S RIBOSOMAL PROTEIN L10A 2 163 6.3E-82
3 g3791.t40 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 2 163 6.3E-82
1 g3791.t40 Pfam PF00687 Ribosomal protein L1p/L10e family 2 159 2.3E-38
5 g3791.t40 ProSitePatterns PS01199 Ribosomal protein L1 signature. 64 83 -
4 g3791.t40 SUPERFAMILY SSF56808 Ribosomal protein L1 2 164 4.19E-54

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed