General information for g9650.t3
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.t3 | TSS | g9650.t3 | 4478269 | 4478269 |
| chr_1 | g9650 | g9650.t3 | isoform | g9650.t3 | 4478281 | 4479451 |
| chr_1 | g9650 | g9650.t3 | exon | g9650.t3.exon1 | 4478281 | 4478539 |
| chr_1 | g9650 | g9650.t3 | exon | g9650.t3.exon2 | 4478711 | 4478935 |
| chr_1 | g9650 | g9650.t3 | cds | g9650.t3.CDS1 | 4478711 | 4478935 |
| chr_1 | g9650 | g9650.t3 | exon | g9650.t3.exon3 | 4479105 | 4479451 |
| chr_1 | g9650 | g9650.t3 | cds | g9650.t3.CDS2 | 4479105 | 4479356 |
| chr_1 | g9650 | g9650.t3 | TTS | g9650.t3 | 4479425 | 4479425 |
Sequences
>g9650.t3 Gene=g9650 Length=831
GGTAATTTCAATAAAACGTGTGAAAGTGAGTAAAATTAATTATTTTTAGTAAGATAAACA
CTGTTTAAGACCTCAAAAACAAATGAAATAATTGCACAAAGATGGCATCTACATTTATTA
ATTGAAAAAACCTTGATTTTATATATAAAACTGATGAAAAATGTGATAATAATTTTTATG
AACCAAAACAAAGTTGAAATTTTTCTAAAATAAAGTTTTATAGAAAAATACATAATTTAT
TCCGTTTTATTTTGATGATATGGCCGATACAGCAGCAAAAACAAAAGCTGCCCCAGCAGC
AAAAAAAGAAAAGAAACCAGCGGCTGAAGCTGCACCAGCAAAACCTAAAGCAAAGGCACC
AGCAGAACCAAAAGCTGTAACTCCACGACCATTCAAACGTTATGGTAGATTATGGGCTAA
GGCTGTCTTTACTGGTTTCAAGCGTGGCTTGAGAAATCAACACGAGAATCACGCTCTTCT
CAAGATTGAAGGATCACGTAGCCGAAAAACATCATTGTTCTATGTTGGTAAACGCTGTGT
ATTTGTTTACAAAGGTAAATCCAAAAAATCATCGCCAACAAATCCAAAACACAAGTCTCG
TCTGCGAGCAATTTGGGGAAAAGTTACCCGACTTCACGGTAATAATGGCAGCGTTCGTGC
TCGCTTCAAGACAAATTTGCCAGGTGATGCAATGGGACATCGTGTAAGAATTATGCTCTA
TCCATCAAGAATTTAAATTTAATCTTGTATATTGGATTTGAAGAACATACAACAAACAGA
ATAAAAACCTCCGTTTGAGAATTCCAATTTAAATTTTTTTTTATTTAAAAA
>g9650.t3 Gene=g9650 Length=158
MADTAAKTKAAPAAKKEKKPAAEAAPAKPKAKAPAEPKAVTPRPFKRYGRLWAKAVFTGF
KRGLRNQHENHALLKIEGSRSRKTSLFYVGKRCVFVYKGKSKKSSPTNPKHKSRLRAIWG
KVTRLHGNNGSVRARFKTNLPGDAMGHRVRIMLYPSRI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9650.t3 | Gene3D | G3DSA:2.40.10.190 | translation elongation factor selb | 48 | 158 | 8.8E-48 |
| 3 | g9650.t3 | Hamap | MF_00573 | 50S ribosomal protein L35Ae [rpl35ae]. | 53 | 152 | 24.194084 |
| 6 | g9650.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 42 | - |
| 7 | g9650.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 10 | 25 | - |
| 2 | g9650.t3 | PANTHER | PTHR10902 | 60S RIBOSOMAL PROTEIN L35A | 44 | 158 | 4.1E-39 |
| 1 | g9650.t3 | Pfam | PF01247 | Ribosomal protein L35Ae | 51 | 152 | 8.8E-39 |
| 5 | g9650.t3 | ProSitePatterns | PS01105 | Ribosomal protein L35Ae signature. | 120 | 141 | - |
| 4 | g9650.t3 | SUPERFAMILY | SSF50447 | Translation proteins | 51 | 152 | 2.0E-32 |
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 transcript has been annotated with K02917 (large subunit ribosomal protein L35Ae)
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.
