General information for g5945.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L34.
Parent gene
- The parent gene g5945 is located on chr_2: 12953160..12956024 (+ 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_2 | g5945 | g5945.t1 | TSS | g5945.t1 | 12952858 | 12952858 |
| chr_2 | g5945 | g5945.t1 | isoform | g5945.t1 | 12952869 | 12953636 |
| chr_2 | g5945 | g5945.t1 | exon | g5945.t1.exon1 | 12952869 | 12952933 |
| chr_2 | g5945 | g5945.t1 | cds | g5945.t1.CDS1 | 12952869 | 12952933 |
| chr_2 | g5945 | g5945.t1 | exon | g5945.t1.exon2 | 12953162 | 12953636 |
| chr_2 | g5945 | g5945.t1 | cds | g5945.t1.CDS2 | 12953162 | 12953636 |
| chr_2 | g5945 | g5945.t1 | TTS | g5945.t1 | 12953711 | 12953711 |
Sequences
>g5945.t1 Gene=g5945 Length=540
ATGGTTCAACGATTAACATTGAGACGACGATTGTCGTATAATACAAAATCAAACAAACGA
CGAATTGTTCGTACTCCTGGTGGACGTCTCGTATATCTTTATTTGAAAAAGAAGCGTACT
GTCCCAAGATGTGCAGTAACAAAGGAAAAATTGCACGGTATCACTCCATCACGCCCAAGT
GAACGTCCTCGTATGGCAAAACGCCTAAAGACAGTCAGACGTGCATATGGTGGTGTCCTT
AGTCACAAAGCTCTTCGTGAACGTATCATTCGTGCATTCTTGATTGATGAACAGAAGGTG
GTGAAAGTATTGAAGGCTGCTCAAGCAACAACAGTGAAAGCACCAAAACCACAAGCTAAA
CCTAAACCAACTGCAAAACCAGCTGCTCCAGCTCCACAAAAAGGTGGTGCAAAGGGTGAT
AAGAAATCTGCTGACAAGAAGAGCGATAAGAAGCCAGTTGCTGCAGACAAAAAATCAGCC
GGAGGAAAGACAGTACCAAAACCATCCGCCGGTGCACCAGCCAAGAAAGCAAAGAAGTAA
>g5945.t1 Gene=g5945 Length=179
MVQRLTLRRRLSYNTKSNKRRIVRTPGGRLVYLYLKKKRTVPRCAVTKEKLHGITPSRPS
ERPRMAKRLKTVRRAYGGVLSHKALRERIIRAFLIDEQKVVKVLKAAQATTVKAPKPQAK
PKPTAKPAAPAPQKGGAKGDKKSADKKSDKKPVAADKKSAGGKTVPKPSAGAPAKKAKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5945.t1 | Gene3D | G3DSA:3.40.1800.40 | - | 39 | 120 | 7.2E-28 |
| 10 | g5945.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 110 | 179 | - |
| 9 | g5945.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 138 | 157 | - |
| 2 | g5945.t1 | PANTHER | PTHR10759:SF0 | FI02850P-RELATED | 1 | 110 | 1.4E-43 |
| 3 | g5945.t1 | PANTHER | PTHR10759 | 60S RIBOSOMAL PROTEIN L34 | 1 | 110 | 1.4E-43 |
| 5 | g5945.t1 | PRINTS | PR01250 | Ribosomal protein L34 signature | 13 | 26 | 1.5E-26 |
| 6 | g5945.t1 | PRINTS | PR01250 | Ribosomal protein L34 signature | 26 | 43 | 1.5E-26 |
| 4 | g5945.t1 | PRINTS | PR01250 | Ribosomal protein L34 signature | 44 | 54 | 1.5E-26 |
| 7 | g5945.t1 | PRINTS | PR01250 | Ribosomal protein L34 signature | 64 | 86 | 1.5E-26 |
| 1 | g5945.t1 | Pfam | PF01199 | Ribosomal protein L34e | 1 | 94 | 3.9E-37 |
| 8 | g5945.t1 | ProSitePatterns | PS01145 | Ribosomal protein L34e signature. | 15 | 28 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5945/g5945.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5945.t1.fa.iupred3.txt does not exist
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 K02915 (large subunit ribosomal protein L34e)
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.
