Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L10.

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 g2519 g2519.t22 TTS g2519.t22 18422182 18422182
chr_3 g2519 g2519.t22 isoform g2519.t22 18422281 18423739
chr_3 g2519 g2519.t22 exon g2519.t22.exon1 18422281 18422368
chr_3 g2519 g2519.t22 cds g2519.t22.CDS1 18422281 18422368
chr_3 g2519 g2519.t22 exon g2519.t22.exon2 18422435 18422614
chr_3 g2519 g2519.t22 cds g2519.t22.CDS2 18422435 18422614
chr_3 g2519 g2519.t22 exon g2519.t22.exon3 18422808 18423113
chr_3 g2519 g2519.t22 cds g2519.t22.CDS3 18422808 18423113
chr_3 g2519 g2519.t22 exon g2519.t22.exon4 18423378 18423417
chr_3 g2519 g2519.t22 cds g2519.t22.CDS4 18423378 18423400
chr_3 g2519 g2519.t22 exon g2519.t22.exon5 18423561 18423739
chr_3 g2519 g2519.t22 TSS g2519.t22 18423810 18423810

Sequences

>g2519.t22 Gene=g2519 Length=793
TATTAATTAAGTAAAAAGTGTTTAATAATGGTTAGCTATTCAGTATTTATTATTATAATA
TAAAGAACAGCTCAATATTTATTGAATTTAGCCAAAAATAAAGAAATTTTTACATGCTTA
AAATTTCATAATTATAACAACGCGTTTCTAATCTTGAATTAATTAATTTCAAGGCAAAAA
TCCTTGAAAGATCAAAATGGGTAGACGTCCAGCACGTTGCTACCGCTACTGCAAAAATAA
ACCGTACCCAAAATCGCGTTTCTGTCGTGGTGTTCCAGATCCGAAAATTCGTATTTTCGA
TTTAGGCAGAAAGAAGGCACTCGTTGAAGATTTTCCTCTTTGTGTGCATCTCGTGTCTGA
TGAATATGAACAGCTAAGCTCTGAAGCTTTGGAAGCAGGACGCATTTGCGCTAACAAATA
TTTGGTAAAATTCTGTGGAAAGGATCAATTCCACATTCGAATGAGACTACATCCATTCCA
TGTCATTCGTATCAACAAGATGTTATCATGTGCTGGAGCTGATAGGCTCCAAACTGGAAT
GCGTGGGGCTTTTGGTAAACCACAAGGCACAGTTGCTAGAGTTCATATTGGTCAGCCAAT
TATGTCTGTTCGTTCAAGTGACCGTTACAAGGCACAAGTCGTCGAAGCATTGCGTCGCGC
TAAATTCAAGTTCCCCGGACGTCAGAAAATCTTTATCTCAAAGAATGATGGTGTTGGCGT
TCAATTCCTCCCAGATCATGGCCCTCTTTCAAAATGGGCAAAGATTCAAGCAAATCAATC
ATATTTGAGTTAA

>g2519.t22 Gene=g2519 Length=198
MGRRPARCYRYCKNKPYPKSRFCRGVPDPKIRIFDLGRKKALVEDFPLCVHLVSDEYEQL
SSEALEAGRICANKYLVKFCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQPIMSVRSSDRYKAQVVEALRRAKFKFPGRQKIFISKNDGVGVQFLPD
HGPLSKWAKIQANQSYLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2519.t22 CDD cd01433 Ribosomal_L16_L10e 41 165 1.28471E-43
5 g2519.t22 Gene3D G3DSA:3.90.1170.10 - 1 197 9.7E-103
2 g2519.t22 PANTHER PTHR11726 60S RIBOSOMAL PROTEIN L10 1 171 1.0E-103
3 g2519.t22 PANTHER PTHR11726:SF29 60S RIBOSOMAL PROTEIN L10-LIKE 1 171 1.0E-103
6 g2519.t22 PIRSF PIRSF005590 RPL10a_RPL10e 1 179 5.5E-91
1 g2519.t22 Pfam PF00252 Ribosomal protein L16p/L10e 12 165 2.4E-36
8 g2519.t22 ProSitePatterns PS01257 Ribosomal protein L10e signature. 108 129 -
4 g2519.t22 SUPERFAMILY SSF54686 Ribosomal protein L16p/L10e 4 171 6.28E-77
9 g2519.t22 TIGRFAM TIGR00279 uL16_euk_arch: ribosomal protein uL16 1 170 3.1E-75

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:0005840 ribosome 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. There were no conditions that were differentially expressed