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.t5 TTS g2519.t5 18422182 18422182
chr_3 g2519 g2519.t5 isoform g2519.t5 18422281 18423400
chr_3 g2519 g2519.t5 exon g2519.t5.exon1 18422281 18422614
chr_3 g2519 g2519.t5 cds g2519.t5.CDS1 18422281 18422614
chr_3 g2519 g2519.t5 exon g2519.t5.exon2 18422808 18423400
chr_3 g2519 g2519.t5 cds g2519.t5.CDS2 18422808 18423139
chr_3 g2519 g2519.t5 TSS g2519.t5 18423810 18423810

Sequences

>g2519.t5 Gene=g2519 Length=927
ATGGGTAGACGTCCAGCACGTTGGTAAGTTTAAAATTACATTACATTCACTTCCTGATTG
CCTTCGCCGACTAAAATTTCATATATTATTCAATTATATGCGATTTTATAAAAGAAAATA
CAAAAAAGAAGGTAGATTAAAGAATTGATTTAGGGTGAGAGGAGAGTTGAAAATTAATCT
ACAATTATTCTCTCAATAATCGATATGACAATATCACAAAATAAACTTTCAAATTCTTTT
TCAGTTTAGAAGAGAAATCTGATGCTATGTCTTATATTTCTTTATAGCTACCGCTACTGC
AAAAATAAACCGTACCCAAAATCGCGTTTCTGTCGTGGTGTTCCAGATCCGAAAATTCGT
ATTTTCGATTTAGGCAGAAAGAAGGCACTCGTTGAAGATTTTCCTCTTTGTGTGCATCTC
GTGTCTGATGAATATGAACAGCTAAGCTCTGAAGCTTTGGAAGCAGGACGCATTTGCGCT
AACAAATATTTGGTAAAATTCTGTGGAAAGGATCAATTCCACATTCGAATGAGACTACAT
CCATTCCATGTCATTCGTATCAACAAGATGTTATCATGTGCTGGAGCTGATAGGCTCCAA
ACTGGAATGCGTGGGGCTTTTGGTAAACCACAAGGCACAGTTGCTAGAGTTCATATTGGT
CAGCCAATTATGTCTGTTCGTTCAAGTGACCGTTACAAGGCACAAGTCGTCGAAGCATTG
CGTCGCGCTAAATTCAAGTTCCCCGGACGTCAGAAAATCTTTATCTCAAAGAAGTGGGGA
TTCACAAAGTTCGACAGAGACGAATTCGAGCGTTTGAAGGAAGAAAAACGCTTCTTACCT
GATGGTGTTGGCGTTCAATTCCTCCCAGATCATGGCCCTCTTTCAAAATGGGCAAAGATT
CAAGCAAATCAATCATATTTGAGTTAA

>g2519.t5 Gene=g2519 Length=221
MLCLIFLYSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGRKKALVEDFPLCVHLVSDEYEQ
LSSEALEAGRICANKYLVKFCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAF
GKPQGTVARVHIGQPIMSVRSSDRYKAQVVEALRRAKFKFPGRQKIFISKKWGFTKFDRD
EFERLKEEKRFLPDGVGVQFLPDHGPLSKWAKIQANQSYLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2519.t5 CDD cd01433 Ribosomal_L16_L10e 42 166 3.36449E-43
6 g2519.t5 Coils Coil Coil 217 221 -
5 g2519.t5 Gene3D G3DSA:3.90.1170.10 - 8 220 3.5E-110
2 g2519.t5 PANTHER PTHR11726 60S RIBOSOMAL PROTEIN L10 9 213 2.4E-114
3 g2519.t5 PANTHER PTHR11726:SF29 60S RIBOSOMAL PROTEIN L10-LIKE 9 213 2.4E-114
1 g2519.t5 Pfam PF00252 Ribosomal protein L16p/L10e 13 166 3.4E-36
8 g2519.t5 ProSitePatterns PS01257 Ribosomal protein L10e signature. 109 130 -
4 g2519.t5 SUPERFAMILY SSF54686 Ribosomal protein L16p/L10e 9 174 1.44E-75
9 g2519.t5 TIGRFAM TIGR00279 uL16_euk_arch: ribosomal protein uL16 9 175 1.7E-71

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.

Raw TPM values