General information for g3791.t60
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.t60 | TTS | g3791.t60 | 27969226 | 27969226 |
| chr_3 | g3791 | g3791.t60 | isoform | g3791.t60 | 27969305 | 27970511 |
| chr_3 | g3791 | g3791.t60 | exon | g3791.t60.exon1 | 27969305 | 27969471 |
| chr_3 | g3791 | g3791.t60 | cds | g3791.t60.CDS1 | 27969436 | 27969471 |
| chr_3 | g3791 | g3791.t60 | exon | g3791.t60.exon2 | 27969532 | 27969853 |
| chr_3 | g3791 | g3791.t60 | cds | g3791.t60.CDS2 | 27969532 | 27969853 |
| chr_3 | g3791 | g3791.t60 | exon | g3791.t60.exon3 | 27970006 | 27970161 |
| chr_3 | g3791 | g3791.t60 | cds | g3791.t60.CDS3 | 27970006 | 27970161 |
| chr_3 | g3791 | g3791.t60 | exon | g3791.t60.exon4 | 27970507 | 27970511 |
| chr_3 | g3791 | g3791.t60 | cds | g3791.t60.CDS4 | 27970507 | 27970511 |
| chr_3 | g3791 | g3791.t60 | TSS | g3791.t60 | 27970567 | 27970567 |
Sequences
>g3791.t60 Gene=g3791 Length=650
ATGTCATCAAAAGTATCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAG
TCTCAAGAAAAGAAGCGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAAC
TACGATCCACAAAAGGATAAGCGTTTCAGCGGCACTGTCAAGTTGAAGCACATTCCACGT
CCAAAAATGCAAGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGCAAAC
GACGTTCCTTTTATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTTGGTC
AAGAAACTCGCCAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACAAATT
CCAAGATTGTTGGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCAACAC
AATGAATCAATGACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAATGAAG
AAGTGTGTCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCTCGCTCAAA
ATGTTCACTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCAAAATGTGC
GTTCACTTCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAA
>g3791.t60 Gene=g3791 Length=172
MSSKVSKDILYECVNEVLTKSQEKKRNFLETVELQIGLKNYDPQKDKRFSGTVKLKHIPR
PKMQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLASESLIKQI
PRLLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQMKKCVSQSLLVMLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3791.t60 | CDD | cd00403 | Ribosomal_L1 | 10 | 161 | 8.4462E-37 |
| 6 | g3791.t60 | Gene3D | G3DSA:3.40.50.790 | - | 61 | 155 | 3.2E-40 |
| 2 | g3791.t60 | PANTHER | PTHR23105:SF154 | 60S RIBOSOMAL PROTEIN L10A | 1 | 164 | 3.4E-81 |
| 3 | g3791.t60 | PANTHER | PTHR23105 | RIBOSOMAL PROTEIN L7AE FAMILY MEMBER | 1 | 164 | 3.4E-81 |
| 7 | g3791.t60 | PIRSF | PIRSF002155 | RPL1p_RPL1a_RPL10e_RPL1o | 1 | 169 | 1.1E-29 |
| 1 | g3791.t60 | Pfam | PF00687 | Ribosomal protein L1p/L10e family | 24 | 162 | 2.6E-25 |
| 5 | g3791.t60 | ProSitePatterns | PS01199 | Ribosomal protein L1 signature. | 117 | 136 | - |
| 4 | g3791.t60 | SUPERFAMILY | SSF56808 | Ribosomal protein L1 | 3 | 167 | 2.62E-46 |
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:0003723 | RNA binding | MF |
| GO:0015934 | large ribosomal subunit | 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. There were no conditions that were differentially expressed