General information for g3791.t39
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L10a.
Parent gene
- The parent gene g3791 is located on chr_3: 27969838..27977146 (- 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 | g3791 | g3791.t39 | TTS | g3791.t39 | 27969226 | 27969226 |
| chr_3 | g3791 | g3791.t39 | isoform | g3791.t39 | 27969305 | 27970511 |
| chr_3 | g3791 | g3791.t39 | exon | g3791.t39.exon1 | 27969305 | 27969475 |
| chr_3 | g3791 | g3791.t39 | cds | g3791.t39.CDS1 | 27969305 | 27969475 |
| chr_3 | g3791 | g3791.t39 | exon | g3791.t39.exon2 | 27969532 | 27969853 |
| chr_3 | g3791 | g3791.t39 | cds | g3791.t39.CDS2 | 27969532 | 27969828 |
| chr_3 | g3791 | g3791.t39 | exon | g3791.t39.exon3 | 27970006 | 27970161 |
| chr_3 | g3791 | g3791.t39 | exon | g3791.t39.exon4 | 27970510 | 27970511 |
| chr_3 | g3791 | g3791.t39 | TSS | g3791.t39 | 27970567 | 27970567 |
Sequences
>g3791.t39 Gene=g3791 Length=651
ATATCAAAAGTATCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAGTCT
CAAGAAAAGAAGCGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAACTAC
GATCCACAAAAGGATAAGCGTTTCAGCGGCACTGTCAAGTTGAAGCACATTCCACGTCCA
AAAATGCAAGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGCAAACGAC
GTTCCTTTTATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTTGGTCAAG
AAACTCGCCAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACAAATTCCA
AGATTGTTGGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCAACACAAT
GAATCAATGACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAATGAAGAAG
GTCTTGTGTCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCTCGCTCAA
AATGTTCACTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCAAAATGTG
CGTTCACTTCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAA
>g3791.t39 Gene=g3791 Length=155
MQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPR
LLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQMKKVLCLSVAVGHVNMTPDELAQN
VHLSINFMVSLLKKHWQNVRSLHIKSSMGPPQRLY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3791.t39 | CDD | cd00403 | Ribosomal_L1 | 1 | 154 | 7.97377E-45 |
| 6 | g3791.t39 | Gene3D | G3DSA:3.40.50.790 | - | 2 | 91 | 2.4E-50 |
| 7 | g3791.t39 | Gene3D | G3DSA:3.30.190.20 | - | 92 | 151 | 2.4E-50 |
| 2 | g3791.t39 | PANTHER | PTHR23105:SF154 | 60S RIBOSOMAL PROTEIN L10A | 2 | 154 | 3.1E-78 |
| 3 | g3791.t39 | PANTHER | PTHR23105 | RIBOSOMAL PROTEIN L7AE FAMILY MEMBER | 2 | 154 | 3.1E-78 |
| 1 | g3791.t39 | Pfam | PF00687 | Ribosomal protein L1p/L10e family | 2 | 150 | 2.8E-37 |
| 5 | g3791.t39 | ProSitePatterns | PS01199 | Ribosomal protein L1 signature. | 55 | 74 | - |
| 4 | g3791.t39 | SUPERFAMILY | SSF56808 | Ribosomal protein L1 | 1 | 155 | 1.44E-51 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K02865 (large subunit ribosomal protein L10Ae)
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.
