General information for g2519.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L10.
Parent gene
- The parent gene g2519 is located on chr_3: 18422281..18423810 (- strand)
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.t1 | TTS | g2519.t1 | 18422182 | 18422182 |
| chr_3 | g2519 | g2519.t1 | isoform | g2519.t1 | 18422281 | 18423400 |
| chr_3 | g2519 | g2519.t1 | exon | g2519.t1.exon1 | 18422281 | 18422614 |
| chr_3 | g2519 | g2519.t1 | cds | g2519.t1.CDS1 | 18422281 | 18422614 |
| chr_3 | g2519 | g2519.t1 | exon | g2519.t1.exon2 | 18422808 | 18423113 |
| chr_3 | g2519 | g2519.t1 | cds | g2519.t1.CDS2 | 18422808 | 18423113 |
| chr_3 | g2519 | g2519.t1 | exon | g2519.t1.exon3 | 18423378 | 18423400 |
| chr_3 | g2519 | g2519.t1 | cds | g2519.t1.CDS3 | 18423378 | 18423400 |
| chr_3 | g2519 | g2519.t1 | TSS | g2519.t1 | 18423810 | 18423810 |
Sequences
>g2519.t1 Gene=g2519 Length=663
ATGGGTAGACGTCCAGCACGTTGCTACCGCTACTGCAAAAATAAACCGTACCCAAAATCG
CGTTTCTGTCGTGGTGTTCCAGATCCGAAAATTCGTATTTTCGATTTAGGCAGAAAGAAG
GCACTCGTTGAAGATTTTCCTCTTTGTGTGCATCTCGTGTCTGATGAATATGAACAGCTA
AGCTCTGAAGCTTTGGAAGCAGGACGCATTTGCGCTAACAAATATTTGGTAAAATTCTGT
GGAAAGGATCAATTCCACATTCGAATGAGACTACATCCATTCCATGTCATTCGTATCAAC
AAGATGTTATCATGTGCTGGAGCTGATAGGCTCCAAACTGGAATGCGTGGGGCTTTTGGT
AAACCACAAGGCACAGTTGCTAGAGTTCATATTGGTCAGCCAATTATGTCTGTTCGTTCA
AGTGACCGTTACAAGGCACAAGTCGTCGAAGCATTGCGTCGCGCTAAATTCAAGTTCCCC
GGACGTCAGAAAATCTTTATCTCAAAGAAGTGGGGATTCACAAAGTTCGACAGAGACGAA
TTCGAGCGTTTGAAGGAAGAAAAACGCTTCTTACCTGATGGTGTTGGCGTTCAATTCCTC
CCAGATCATGGCCCTCTTTCAAAATGGGCAAAGATTCAAGCAAATCAATCATATTTGAGT
TAA
>g2519.t1 Gene=g2519 Length=220
MGRRPARCYRYCKNKPYPKSRFCRGVPDPKIRIFDLGRKKALVEDFPLCVHLVSDEYEQL
SSEALEAGRICANKYLVKFCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQPIMSVRSSDRYKAQVVEALRRAKFKFPGRQKIFISKKWGFTKFDRDE
FERLKEEKRFLPDGVGVQFLPDHGPLSKWAKIQANQSYLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2519.t1 | CDD | cd01433 | Ribosomal_L16_L10e | 41 | 165 | 8.57247E-43 |
| 5 | g2519.t1 | Gene3D | G3DSA:3.90.1170.10 | - | 1 | 219 | 7.3E-117 |
| 2 | g2519.t1 | PANTHER | PTHR11726 | 60S RIBOSOMAL PROTEIN L10 | 1 | 212 | 3.3E-120 |
| 3 | g2519.t1 | PANTHER | PTHR11726:SF29 | 60S RIBOSOMAL PROTEIN L10-LIKE | 1 | 212 | 3.3E-120 |
| 6 | g2519.t1 | PIRSF | PIRSF005590 | RPL10a_RPL10e | 1 | 182 | 2.8E-94 |
| 1 | g2519.t1 | Pfam | PF00252 | Ribosomal protein L16p/L10e | 12 | 165 | 3.3E-36 |
| 8 | g2519.t1 | ProSitePatterns | PS01257 | Ribosomal protein L10e signature. | 108 | 129 | - |
| 4 | g2519.t1 | SUPERFAMILY | SSF54686 | Ribosomal protein L16p/L10e | 4 | 173 | 1.7E-78 |
| 9 | g2519.t1 | TIGRFAM | TIGR00279 | uL16_euk_arch: ribosomal protein uL16 | 1 | 174 | 3.2E-76 |
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 transcript has been annotated with K02866 (large subunit ribosomal protein L10e)
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.
