General information for g3791.t3
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.t3 | isoform | g3791.t3 | 27967328 | 27970511 |
| chr_3 | g3791 | g3791.t3 | exon | g3791.t3.exon1 | 27967328 | 27967336 |
| chr_3 | g3791 | g3791.t3 | exon | g3791.t3.exon2 | 27969184 | 27969475 |
| chr_3 | g3791 | g3791.t3 | cds | g3791.t3.CDS1 | 27969305 | 27969475 |
| chr_3 | g3791 | g3791.t3 | exon | g3791.t3.exon3 | 27969532 | 27969853 |
| chr_3 | g3791 | g3791.t3 | cds | g3791.t3.CDS2 | 27969532 | 27969853 |
| chr_3 | g3791 | g3791.t3 | exon | g3791.t3.exon4 | 27970002 | 27970161 |
| chr_3 | g3791 | g3791.t3 | cds | g3791.t3.CDS3 | 27970002 | 27970003 |
| chr_3 | g3791 | g3791.t3 | exon | g3791.t3.exon5 | 27970507 | 27970511 |
| chr_3 | g3791 | g3791.t3 | TSS | g3791.t3 | 27970567 | 27970567 |
| chr_3 | g3791 | g3791.t3 | TTS | g3791.t3 | NA | NA |
Sequences
>g3791.t3 Gene=g3791 Length=788
ATGTCATCAAAAGTATCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAG
TCTCAAGAAAAGAAGCGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAAC
TACGATCCACAAAAGGATAAGCGTTTCAGCGGCACTGTCAAGTATGTTGAAGCACATTCC
ACGTCCAAAAATGCAAGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGC
AAACGACGTTCCTTTTATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTT
GGTCAAGAAACTCGCCAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACA
AATTCCAAGATTGTTGGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCA
ACACAATGAATCAATGACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAAT
GAAGAAGGTCTTGTGTCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCT
CGCTCAAAATGTTCACTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCA
AAATGTGCGTTCACTTCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAAAA
CACTTGCATATTACTGTGTTTTTGTATCAATGAAAAATTAACAATTTCAAATAAAATCTA
GAAATTGAACTGAAACTAATTTTATCATAGTTTAACTGTCATTTTATTTTTAAACTTAAC
TTCTCACA
>g3791.t3 Gene=g3791 Length=164
MLKHIPRPKMQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLAS
ESLIKQIPRLLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQMKKVLCLSVAVGHVN
MTPDELAQNVHLSINFMVSLLKKHWQNVRSLHIKSSMGPPQRLY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3791.t3 | CDD | cd00403 | Ribosomal_L1 | 2 | 163 | 1.49583E-47 |
| 7 | g3791.t3 | Gene3D | G3DSA:3.30.190.20 | - | 2 | 160 | 2.9E-52 |
| 6 | g3791.t3 | Gene3D | G3DSA:3.40.50.790 | - | 10 | 100 | 2.9E-52 |
| 2 | g3791.t3 | PANTHER | PTHR23105:SF154 | 60S RIBOSOMAL PROTEIN L10A | 2 | 163 | 6.3E-82 |
| 3 | g3791.t3 | PANTHER | PTHR23105 | RIBOSOMAL PROTEIN L7AE FAMILY MEMBER | 2 | 163 | 6.3E-82 |
| 1 | g3791.t3 | Pfam | PF00687 | Ribosomal protein L1p/L10e family | 2 | 159 | 2.3E-38 |
| 5 | g3791.t3 | ProSitePatterns | PS01199 | Ribosomal protein L1 signature. | 64 | 83 | - |
| 4 | g3791.t3 | SUPERFAMILY | SSF56808 | Ribosomal protein L1 | 2 | 164 | 4.19E-54 |
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.
