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.t91 TTS g3791.t91 27969226 27969226
chr_3 g3791 g3791.t91 isoform g3791.t91 27969305 27970567
chr_3 g3791 g3791.t91 exon g3791.t91.exon1 27969305 27969482
chr_3 g3791 g3791.t91 cds g3791.t91.CDS1 27969305 27969482
chr_3 g3791 g3791.t91 exon g3791.t91.exon2 27969539 27969853
chr_3 g3791 g3791.t91 cds g3791.t91.CDS2 27969539 27969853
chr_3 g3791 g3791.t91 exon g3791.t91.exon3 27970006 27970161
chr_3 g3791 g3791.t91 cds g3791.t91.CDS3 27970006 27970161
chr_3 g3791 g3791.t91 exon g3791.t91.exon4 27970507 27970567
chr_3 g3791 g3791.t91 cds g3791.t91.CDS4 27970507 27970511
chr_3 g3791 g3791.t91 TSS g3791.t91 27970567 27970567

Sequences

>g3791.t91 Gene=g3791 Length=710
CTTTTCCTTCAAGTTTTCGTTGCAGAAAGAGGTGTGCAGCAAAAATTTAGTTAAAAATGT
CATCAAAAGTATCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAGTCTC
AAGAAAAGAAGCGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAACTACG
ATCCACAAAAGGATAAGCGTTTCAGCGGCACTGTCAAGTTGAAGCACATTCCACGTCCAA
AAATGCAAGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGCAAACGACG
TTCCTTTTATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTTGGTCAAGA
AACTCGCCAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACAAATTCCAA
GATTGTTGGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCAACACAATG
AATCAATGACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAATTAAAAAGG
TCTTGTGTCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCTCGCTCAAA
ATGTTCACTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCAAAATGTGC
GTTCACTTCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAA

>g3791.t91 Gene=g3791 Length=217
MSSKVSKDILYECVNEVLTKSQEKKRNFLETVELQIGLKNYDPQKDKRFSGTVKLKHIPR
PKMQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLASESLIKQI
PRLLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQIKKVLCLSVAVGHVNMTPDELA
QNVHLSINFMVSLLKKHWQNVRSLHIKSSMGPPQRLY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3791.t91 CDD cd00403 Ribosomal_L1 10 216 4.28658E-63
7 g3791.t91 Gene3D G3DSA:3.30.190.20 - 23 211 6.9E-68
6 g3791.t91 Gene3D G3DSA:3.40.50.790 - 63 152 6.9E-68
2 g3791.t91 PANTHER PTHR23105:SF154 60S RIBOSOMAL PROTEIN L10A 1 216 1.1E-108
3 g3791.t91 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 1 216 1.1E-108
8 g3791.t91 PIRSF PIRSF002155 RPL1p_RPL1a_RPL10e_RPL1o 1 217 2.6E-46
1 g3791.t91 Pfam PF00687 Ribosomal protein L1p/L10e family 24 212 6.3E-46
5 g3791.t91 ProSitePatterns PS01199 Ribosomal protein L1 signature. 117 136 -
4 g3791.t91 SUPERFAMILY SSF56808 Ribosomal protein L1 3 217 4.84E-68

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

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