Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t24 TTS g3791.t24 27969226 27969226
chr_3 g3791 g3791.t24 isoform g3791.t24 27969305 27970161
chr_3 g3791 g3791.t24 exon g3791.t24.exon1 27969305 27969471
chr_3 g3791 g3791.t24 cds g3791.t24.CDS1 27969436 27969471
chr_3 g3791 g3791.t24 exon g3791.t24.exon2 27969532 27969853
chr_3 g3791 g3791.t24 cds g3791.t24.CDS2 27969532 27969853
chr_3 g3791 g3791.t24 exon g3791.t24.exon3 27970002 27970161
chr_3 g3791 g3791.t24 cds g3791.t24.CDS3 27970002 27970003
chr_3 g3791 g3791.t24 TSS g3791.t24 27970567 27970567

Sequences

>g3791.t24 Gene=g3791 Length=649
ATCAAAAGTATCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAGTCTCA
AGAAAAGAAGCGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAACTACGA
TCCACAAAAGGATAAGCGTTTCAGCGGCACTGTCAAGTATGTTGAAGCACATTCCACGTC
CAAAAATGCAAGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGCAAACG
ACGTTCCTTTTATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTTGGTCA
AGAAACTCGCCAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACAAATTC
CAAGATTGTTGGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCAACACA
ATGAATCAATGACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAATGAAGA
AGTGTGTCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCTCGCTCAAAA
TGTTCACTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCAAAATGTGCG
TTCACTTCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAA

>g3791.t24 Gene=g3791 Length=119
MLKHIPRPKMQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLAS
ESLIKQIPRLLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQMKKCVSQSLLVMLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g3791.t24 CDD cd00403 Ribosomal_L1 2 111 1.86591E-20
6 g3791.t24 Gene3D G3DSA:3.40.50.790 - 8 102 1.0E-40
2 g3791.t24 PANTHER PTHR23105:SF154 60S RIBOSOMAL PROTEIN L10A 2 111 1.4E-53
3 g3791.t24 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 2 111 1.4E-53
1 g3791.t24 Pfam PF00687 Ribosomal protein L1p/L10e family 2 109 9.7E-18
5 g3791.t24 ProSitePatterns PS01199 Ribosomal protein L1 signature. 64 83 -
4 g3791.t24 SUPERFAMILY SSF56808 Ribosomal protein L1 2 113 1.7E-31

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

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