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.t33 TTS g3791.t33 27969226 27969226
chr_3 g3791 g3791.t33 isoform g3791.t33 27969305 27970511
chr_3 g3791 g3791.t33 exon g3791.t33.exon1 27969305 27969479
chr_3 g3791 g3791.t33 cds g3791.t33.CDS1 27969441 27969479
chr_3 g3791 g3791.t33 exon g3791.t33.exon2 27969532 27969853
chr_3 g3791 g3791.t33 cds g3791.t33.CDS2 27969532 27969853
chr_3 g3791 g3791.t33 exon g3791.t33.exon3 27970006 27970161
chr_3 g3791 g3791.t33 cds g3791.t33.CDS3 27970006 27970161
chr_3 g3791 g3791.t33 exon g3791.t33.exon4 27970507 27970511
chr_3 g3791 g3791.t33 cds g3791.t33.CDS4 27970507 27970511
chr_3 g3791 g3791.t33 TSS g3791.t33 27970567 27970567

Sequences

>g3791.t33 Gene=g3791 Length=658
ATGTCATCAAAAGTATCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAG
TCTCAAGAAAAGAAGCGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAAC
TACGATCCACAAAAGGATAAGCGTTTCAGCGGCACTGTCAAGTTGAAGCACATTCCACGT
CCAAAAATGCAAGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGCAAAC
GACGTTCCTTTTATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTTGGTC
AAGAAACTCGCCAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACAAATT
CCAAGATTGTTGGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCAACAC
AATGAATCAATGACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAATGAAG
AAGAAAGGTCTTGTGTCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCT
CGCTCAAAATGTTCACTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCA
AAATGTGCGTTCACTTCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAA

>g3791.t33 Gene=g3791 Length=173
MSSKVSKDILYECVNEVLTKSQEKKRNFLETVELQIGLKNYDPQKDKRFSGTVKLKHIPR
PKMQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLASESLIKQI
PRLLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQMKKKGLVSLSRCWSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3791.t33 CDD cd00403 Ribosomal_L1 10 166 1.4364E-38
7 g3791.t33 Gene3D G3DSA:3.30.190.20 - 23 166 3.4E-51
6 g3791.t33 Gene3D G3DSA:3.40.50.790 - 63 152 3.4E-51
2 g3791.t33 PANTHER PTHR23105:SF154 60S RIBOSOMAL PROTEIN L10A 1 162 9.3E-81
3 g3791.t33 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 1 162 9.3E-81
8 g3791.t33 PIRSF PIRSF002155 RPL1p_RPL1a_RPL10e_RPL1o 1 168 9.0E-31
1 g3791.t33 Pfam PF00687 Ribosomal protein L1p/L10e family 24 166 6.6E-26
5 g3791.t33 ProSitePatterns PS01199 Ribosomal protein L1 signature. 117 136 -
4 g3791.t33 SUPERFAMILY SSF56808 Ribosomal protein L1 3 166 1.28E-46

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:0003723 RNA binding MF
GO:0015934 large ribosomal subunit 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. There were no conditions that were differentially expressed