General information for g9650.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L35a.
Parent gene
- The parent gene g9650 is located on chr_1: 4479451..4481309 (+ 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_1 | g9650 | g9650.t12 | TSS | g9650.t12 | 4478269 | 4478269 |
| chr_1 | g9650 | g9650.t12 | isoform | g9650.t12 | 4478287 | 4479303 |
| chr_1 | g9650 | g9650.t12 | exon | g9650.t12.exon1 | 4478287 | 4478305 |
| chr_1 | g9650 | g9650.t12 | cds | g9650.t12.CDS1 | 4478287 | 4478305 |
| chr_1 | g9650 | g9650.t12 | exon | g9650.t12.exon2 | 4478739 | 4478935 |
| chr_1 | g9650 | g9650.t12 | cds | g9650.t12.CDS2 | 4478739 | 4478935 |
| chr_1 | g9650 | g9650.t12 | exon | g9650.t12.exon3 | 4479105 | 4479303 |
| chr_1 | g9650 | g9650.t12 | cds | g9650.t12.CDS3 | 4479105 | 4479302 |
| chr_1 | g9650 | g9650.t12 | TTS | g9650.t12 | 4479425 | 4479425 |
Sequences
>g9650.t12 Gene=g9650 Length=415
TTCAATAAAACGTGTGAAACTGCCCCAGCAGCAAAAAAAGAAAAGAAACCAGCGGCTGAA
GCTGCACCAGCAAAACCTAAAGCAAAGGCACCAGCAGAACCAAAAGCTGTAACTCCACGA
CCATTCAAACGTTATGGTAGATTATGGGCTAAGGCTGTCTTTACTGGTTTCAAGCGTGGC
TTGAGAAATCAACACGAGAATCACGCTCTTCTCAAGATTGAAGGATCACGTAGCCGAAAA
ACATCATTGTTCTATGTTGGTAAACGCTGTGTATTTGTTTACAAAGGTAAATCCAAAAAA
TCATCGCCAACAAATCCAAAACACAAGTCTCGTCTGCGAGCAATTTGGGGAAAAGTTACC
CGACTTCACGGTAATAATGGCAGCGTTCGTGCTCGCTTCAAGACAAATTTGCCAG
>g9650.t12 Gene=g9650 Length=138
FNKTCETAPAAKKEKKPAAEAAPAKPKAKAPAEPKAVTPRPFKRYGRLWAKAVFTGFKRG
LRNQHENHALLKIEGSRSRKTSLFYVGKRCVFVYKGKSKKSSPTNPKHKSRLRAIWGKVT
RLHGNNGSVRARFKTNLP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9650.t12 | Gene3D | G3DSA:2.40.10.190 | translation elongation factor selb | 45 | 138 | 1.0E-37 |
| 6 | g9650.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 39 | - |
| 5 | g9650.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 8 | 22 | - |
| 2 | g9650.t12 | PANTHER | PTHR10902 | 60S RIBOSOMAL PROTEIN L35A | 47 | 138 | 7.0E-31 |
| 1 | g9650.t12 | Pfam | PF01247 | Ribosomal protein L35Ae | 48 | 138 | 3.2E-33 |
| 4 | g9650.t12 | ProSitePatterns | PS01105 | Ribosomal protein L35Ae signature. | 117 | 138 | - |
| 3 | g9650.t12 | SUPERFAMILY | SSF50447 | Translation proteins | 48 | 138 | 3.53E-27 |
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 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.
