General information for g3343.t29
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L4.
Parent gene
- The parent gene g3343 is located on chr_3: 24754125..24754849 (- 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 | g3343 | g3343.t29 | TTS | g3343.t29 | 24752884 | 24752884 |
| chr_3 | g3343 | g3343.t29 | isoform | g3343.t29 | 24753005 | 24754288 |
| chr_3 | g3343 | g3343.t29 | exon | g3343.t29.exon1 | 24753005 | 24753522 |
| chr_3 | g3343 | g3343.t29 | cds | g3343.t29.CDS1 | 24753005 | 24753522 |
| chr_3 | g3343 | g3343.t29 | exon | g3343.t29.exon2 | 24753574 | 24753703 |
| chr_3 | g3343 | g3343.t29 | cds | g3343.t29.CDS2 | 24753574 | 24753703 |
| chr_3 | g3343 | g3343.t29 | exon | g3343.t29.exon3 | 24753929 | 24754053 |
| chr_3 | g3343 | g3343.t29 | cds | g3343.t29.CDS3 | 24753929 | 24754053 |
| chr_3 | g3343 | g3343.t29 | exon | g3343.t29.exon4 | 24754107 | 24754288 |
| chr_3 | g3343 | g3343.t29 | cds | g3343.t29.CDS4 | 24754107 | 24754245 |
| chr_3 | g3343 | g3343.t29 | TSS | g3343.t29 | 24754851 | 24754851 |
Sequences
>g3343.t29 Gene=g3343 Length=955
TGGTGGTGGTACTCATCGTTCAGGTCAGGGTGCTTTCGGAAATATGTGTCGTGGAGGTCG
CATGTTCGCTCCAACTAAACCATGGCGTAGATGGCATCGTCGCATTAATGTCAACTTGAA
ACGTTATGCAGTTGTTTCAGCTGTTGCTGCATCAGGCGTTCCAGCTCTTGTTCAAGCTCG
AGGACATATTATTGACGGAATTGCTGAACTTCCATTGGTTGTCTCAGATAAAGTTCAAGA
ATACAACAAGACCAAACAAGCTGTTTTGTTCTTACGTCGTAACAAGTTGTGGGGAGATGT
TTTGAAAGTTTATCGTTCAAAACGCTTTAGAGCTGGTCGTGGTAAAATGCGAAATCGTCG
TCGTATTCAACGTCGTGGACCATTAATTGTTTACTCGAAGGATGATGGCTTGCGTCGTGC
ATTCCGTAATATTCCCGGTGGACATCTTGGACGATTGATTGTTTGGACCGAAGGCGCTTT
CAAGCATTTGAATGCATTGTTTGGAACATGGAGTGAGCCTTCAACAGTGAAAAAGGCTTA
CAATCTGCCACATCCAATTATGTCTAACACTGATTTGACTCGCTTGCTCAAATCACAAGA
AATCAAGAGCGTTTTGAATGCACCTAAGAAGAGAGTTTTCCATCGTGTACGCCGCTTGAA
TCCATTGAAGAACGCCAGACAAAAGACCAAGTTGAATCCATATTCAGAAGTTACTCGTCG
TCGTGCATTGTTGGCTAAAGAAAAGCGAAAGTATGAGACACAAATTGCCAAGGCAAAGAA
GAAGAAGGTCGAACTCAAGAGCAATCATCCAGCTATTGTGTATCAAAAGAATGTTGCTAA
TCGTTTGAAGCTCTTAGCTGCATCAAAGAAAGCTAGACAAGCTCGCGCTGCTGAAAAGAA
AAAAGCTGCTGCTGGAAAGAAAGCAACAAAAAAGACCGCAGCCAAGAAAAAGTAA
>g3343.t29 Gene=g3343 Length=303
MCRGGRMFAPTKPWRRWHRRINVNLKRYAVVSAVAASGVPALVQARGHIIDGIAELPLVV
SDKVQEYNKTKQAVLFLRRNKLWGDVLKVYRSKRFRAGRGKMRNRRRIQRRGPLIVYSKD
DGLRRAFRNIPGGHLGRLIVWTEGAFKHLNALFGTWSEPSTVKKAYNLPHPIMSNTDLTR
LLKSQEIKSVLNAPKKRVFHRVRRLNPLKNARQKTKLNPYSEVTRRRALLAKEKRKYETQ
IAKAKKKKVELKSNHPAIVYQKNVANRLKLLAASKKARQARAAEKKKAAAGKKATKKTAA
KKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3343.t29 | Coils | Coil | Coil | 227 | 254 | - |
| 6 | g3343.t29 | Gene3D | G3DSA:3.40.1370.10 | - | 1 | 193 | 2.9E-78 |
| 14 | g3343.t29 | MobiDBLite | mobidb-lite | consensus disorder prediction | 275 | 303 | - |
| 3 | g3343.t29 | PANTHER | PTHR19431 | 60S RIBOSOMAL PROTEIN L4 | 1 | 283 | 1.3E-99 |
| 4 | g3343.t29 | PANTHER | PTHR19431:SF0 | 60S RIBOSOMAL PROTEIN L4 | 1 | 283 | 1.3E-99 |
| 1 | g3343.t29 | Pfam | PF00573 | Ribosomal protein L4/L1 family | 1 | 132 | 1.7E-14 |
| 2 | g3343.t29 | Pfam | PF14374 | 60S ribosomal protein L4 C-terminal domain | 164 | 236 | 8.0E-24 |
| 9 | g3343.t29 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 45 | - |
| 10 | g3343.t29 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 28 | - |
| 11 | g3343.t29 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 29 | 37 | - |
| 12 | g3343.t29 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 38 | 45 | - |
| 8 | g3343.t29 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 46 | 303 | - |
| 13 | g3343.t29 | ProSitePatterns | PS00939 | Ribosomal protein L1e signature. | 22 | 48 | - |
| 5 | g3343.t29 | SUPERFAMILY | SSF52166 | Ribosomal protein L4 | 1 | 150 | 1.23E-45 |
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.
