General information for g3791.t30
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t30 | TTS | g3791.t30 | 27969226 | 27969226 |
| chr_3 | g3791 | g3791.t30 | isoform | g3791.t30 | 27969305 | 27970161 |
| chr_3 | g3791 | g3791.t30 | exon | g3791.t30.exon1 | 27969305 | 27969853 |
| chr_3 | g3791 | g3791.t30 | cds | g3791.t30.CDS1 | 27969436 | 27969828 |
| chr_3 | g3791 | g3791.t30 | exon | g3791.t30.exon2 | 27970006 | 27970161 |
| chr_3 | g3791 | g3791.t30 | TSS | g3791.t30 | 27970567 | 27970567 |
Sequences
>g3791.t30 Gene=g3791 Length=705
ATCAAAAGTATCAAAGGATATTCTTTATGAATGCGTCAATGAAGTATTGACAAAGTCTCA
AGAAAAGAAGCGTAACTTCTTGGAGACTGTTGAATTGCAAATTGGATTGAAGAACTACGA
TCCACAAAAGGATAAGCGTTTCAGCGGCACTGTCAAGTTGAAGCACATTCCACGTCCAAA
AATGCAAGTTTGCATTTTGGGAGATCAACAACATTGTGACGAAGCTAAGGCAAACGACGT
TCCTTTTATGGACGCTGAAGCTTTGAAAAAACTCAACAAAAACAAGAAGTTGGTCAAGAA
ACTCGCCAAGAAATACGATGCTTTCCTTGCTTCAGAATCATTGATTAAACAAATTCCAAG
ATTGTTGGGTCCAGGTTTGAACAAGGCTGGTAAATTCCCTGGTTTATTGCAACACAATGA
ATCAATGACTCAAAAAATTGATGAAGTTAAGGCAACAATCAAGTTCCAAATGAAGAAGGT
GAGGCTGTTGTTAGTTTTTGTTATTTTATTTAACTTATTTGTATTTTTAAAAAGGTCTTG
TGTCTCTCAGTCGCTGTTGGTCATGTTAACATGACACCTGATGAGCTCGCTCAAAATGTT
CACTTGTCAATCAACTTCATGGTTTCGCTTTTGAAGAAGCACTGGCAAAATGTGCGTTCA
CTTCATATTAAATCATCAATGGGACCACCACAACGTCTCTATTAA
>g3791.t30 Gene=g3791 Length=130
MQVCILGDQQHCDEAKANDVPFMDAEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPR
LLGPGLNKAGKFPGLLQHNESMTQKIDEVKATIKFQMKKVRLLLVFVILFNLFVFLKRSC
VSQSLLVMLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3791.t30 | Gene3D | G3DSA:3.40.50.790 | - | 1 | 93 | 1.5E-39 |
| 2 | g3791.t30 | PANTHER | PTHR23105:SF154 | 60S RIBOSOMAL PROTEIN L10A | 2 | 107 | 5.0E-51 |
| 3 | g3791.t30 | PANTHER | PTHR23105 | RIBOSOMAL PROTEIN L7AE FAMILY MEMBER | 2 | 107 | 5.0E-51 |
| 1 | g3791.t30 | Pfam | PF00687 | Ribosomal protein L1p/L10e family | 2 | 101 | 3.0E-16 |
| 8 | g3791.t30 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 99 | - |
| 10 | g3791.t30 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 100 | 116 | - |
| 9 | g3791.t30 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 117 | 130 | - |
| 6 | g3791.t30 | ProSitePatterns | PS01199 | Ribosomal protein L1 signature. | 55 | 74 | - |
| 5 | g3791.t30 | SUPERFAMILY | SSF56808 | Ribosomal protein L1 | 1 | 106 | 9.81E-29 |
| 4 | g3791.t30 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 100 | 122 | - |
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 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.
