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.t7 TTS g2519.t7 18422182 18422182
chr_3 g2519 g2519.t7 isoform g2519.t7 18422281 18423400
chr_3 g2519 g2519.t7 exon g2519.t7.exon1 18422281 18422355
chr_3 g2519 g2519.t7 cds g2519.t7.CDS1 18422286 18422355
chr_3 g2519 g2519.t7 exon g2519.t7.exon2 18422420 18422614
chr_3 g2519 g2519.t7 cds g2519.t7.CDS2 18422420 18422614
chr_3 g2519 g2519.t7 exon g2519.t7.exon3 18422808 18423400
chr_3 g2519 g2519.t7 cds g2519.t7.CDS3 18422808 18423139
chr_3 g2519 g2519.t7 TSS g2519.t7 18423810 18423810

Sequences

>g2519.t7 Gene=g2519 Length=863
ATGGGTAGACGTCCAGCACGTTGGTAAGTTTAAAATTACATTACATTCACTTCCTGATTG
CCTTCGCCGACTAAAATTTCATATATTATTCAATTATATGCGATTTTATAAAAGAAAATA
CAAAAAAGAAGGTAGATTAAAGAATTGATTTAGGGTGAGAGGAGAGTTGAAAATTAATCT
ACAATTATTCTCTCAATAATCGATATGACAATATCACAAAATAAACTTTCAAATTCTTTT
TCAGTTTAGAAGAGAAATCTGATGCTATGTCTTATATTTCTTTATAGCTACCGCTACTGC
AAAAATAAACCGTACCCAAAATCGCGTTTCTGTCGTGGTGTTCCAGATCCGAAAATTCGT
ATTTTCGATTTAGGCAGAAAGAAGGCACTCGTTGAAGATTTTCCTCTTTGTGTGCATCTC
GTGTCTGATGAATATGAACAGCTAAGCTCTGAAGCTTTGGAAGCAGGACGCATTTGCGCT
AACAAATATTTGGTAAAATTCTGTGGAAAGGATCAATTCCACATTCGAATGAGACTACAT
CCATTCCATGTCATTCGTATCAACAAGATGTTATCATGTGCTGGAGCTGATAGGCTCCAA
ACTGGAATGCGTGGGGCTTTTGGTAAACCACAAGGCACAGTTGCTAGAGTTCATATTGGT
CAGCCAATTATGTCTGTTCGTTCAAGTGACCGTTACAAGGCACAAGTCGTCGAAGCATTG
CGTCGCGCTAAATTCAAGTTCCCCGGACGTCAGAAAATCTTTATCTCAAAGAAGTGGGGA
TTCACAAAGTTCAATTCCTCCCAGATCATGGCCCTCTTTCAAAATGGGCAAAGATTCAAG
CAAATCAATCATATTTGAGTTAA

>g2519.t7 Gene=g2519 Length=198
MLCLIFLYSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGRKKALVEDFPLCVHLVSDEYEQ
LSSEALEAGRICANKYLVKFCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAF
GKPQGTVARVHIGQPIMSVRSSDRYKAQVVEALRRAKFKFPGRQKIFISKKWGFTKFNSS
QIMALFQNGQRFKQINHI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2519.t7 CDD cd01433 Ribosomal_L16_L10e 42 166 1.48978E-42
5 g2519.t7 Gene3D G3DSA:3.90.1170.10 - 8 197 5.6E-98
2 g2519.t7 PANTHER PTHR11726 60S RIBOSOMAL PROTEIN L10 9 181 8.4E-103
3 g2519.t7 PANTHER PTHR11726:SF29 60S RIBOSOMAL PROTEIN L10-LIKE 9 181 8.4E-103
6 g2519.t7 PIRSF PIRSF005590 RPL10a_RPL10e 7 183 6.4E-88
1 g2519.t7 Pfam PF00252 Ribosomal protein L16p/L10e 13 166 2.4E-36
8 g2519.t7 ProSitePatterns PS01257 Ribosomal protein L10e signature. 109 130 -
4 g2519.t7 SUPERFAMILY SSF54686 Ribosomal protein L16p/L10e 9 174 1.01E-75
9 g2519.t7 TIGRFAM TIGR00279 uL16_euk_arch: ribosomal protein uL16 9 175 1.3E-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

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.

Raw TPM values