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.t78 TTS g3791.t78 27969226 27969226
chr_3 g3791 g3791.t78 isoform g3791.t78 27969305 27970511
chr_3 g3791 g3791.t78 exon g3791.t78.exon1 27969305 27969468
chr_3 g3791 g3791.t78 cds g3791.t78.CDS1 27969436 27969468
chr_3 g3791 g3791.t78 exon g3791.t78.exon2 27969532 27969853
chr_3 g3791 g3791.t78 cds g3791.t78.CDS2 27969532 27969853
chr_3 g3791 g3791.t78 exon g3791.t78.exon3 27970006 27970161
chr_3 g3791 g3791.t78 cds g3791.t78.CDS3 27970006 27970161
chr_3 g3791 g3791.t78 exon g3791.t78.exon4 27970507 27970511
chr_3 g3791 g3791.t78 cds g3791.t78.CDS4 27970507 27970511
chr_3 g3791 g3791.t78 TSS g3791.t78 27970567 27970567

Sequences

>g3791.t78 Gene=g3791 Length=647
ATGTCATCAAAAGTATCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAG
TCTCAAGAAAAGAAGCGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAAC
TACGATCCACAAAAGGATAAGCGTTTCAGCGGCACTGTCAAGTTGAAGCACATTCCACGT
CCAAAAATGCAAGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGCAAAC
GACGTTCCTTTTATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTTGGTC
AAGAAACTCGCCAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACAAATT
CCAAGATTGTTGGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCAACAC
AATGAATCAATGACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAATGAAG
AAGGTCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCTCGCTCAAAATG
TTCACTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCAAAATGTGCGTT
CACTTCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAA

>g3791.t78 Gene=g3791 Length=171
MSSKVSKDILYECVNEVLTKSQEKKRNFLETVELQIGLKNYDPQKDKRFSGTVKLKHIPR
PKMQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLASESLIKQI
PRLLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQMKKVSQSLLVMLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3791.t78 CDD cd00403 Ribosomal_L1 10 162 1.28495E-36
7 g3791.t78 Gene3D G3DSA:3.30.190.20 - 23 162 1.6E-50
6 g3791.t78 Gene3D G3DSA:3.40.50.790 - 63 152 1.6E-50
2 g3791.t78 PANTHER PTHR23105:SF154 60S RIBOSOMAL PROTEIN L10A 1 163 1.7E-81
3 g3791.t78 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 1 163 1.7E-81
8 g3791.t78 PIRSF PIRSF002155 RPL1p_RPL1a_RPL10e_RPL1o 1 165 2.6E-29
1 g3791.t78 Pfam PF00687 Ribosomal protein L1p/L10e family 24 162 5.2E-25
5 g3791.t78 ProSitePatterns PS01199 Ribosomal protein L1 signature. 117 136 -
4 g3791.t78 SUPERFAMILY SSF56808 Ribosomal protein L1 3 163 4.06E-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