General information for g3343.t54
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t54 | TTS | g3343.t54 | 24752884 | 24752884 |
| chr_3 | g3343 | g3343.t54 | isoform | g3343.t54 | 24753005 | 24754773 |
| chr_3 | g3343 | g3343.t54 | exon | g3343.t54.exon1 | 24753005 | 24753214 |
| chr_3 | g3343 | g3343.t54 | exon | g3343.t54.exon2 | 24753270 | 24753703 |
| chr_3 | g3343 | g3343.t54 | exon | g3343.t54.exon3 | 24754039 | 24754773 |
| chr_3 | g3343 | g3343.t54 | cds | g3343.t54.CDS1 | 24754093 | 24754398 |
| chr_3 | g3343 | g3343.t54 | TSS | g3343.t54 | 24754851 | 24754851 |
Sequences
>g3343.t54 Gene=g3343 Length=1379
ATGGTTAGTATTTGTAAATATTCATTAGTTAATTGCATAAAGTTGCGTGTGCATATCGAT
TTTGTGCAATTACTGAGCGTTTAAATTGAAAAAATTAGGAAAAATATTTTTAATAATTTT
TGCATGTGGCAAATAGTAATTTTGACTATTTTCTATTGTTTCCAGCACTAAAATCGTTGC
ACAAACTTAAAGATAAATCATATAAAAATGTATTTTAATTGATATTTCTTTTAATTTTAG
AGTAAATCAGCTGCTCGTCCGCTCGTCAGTGTTTATACTGACAAAAGTGAGGTTATTAAA
GATACAACAATTCCATTGCCTGCAATTTTCAAGGCTCCAATTCGCCCAGATGTCGTCAAT
GATGTACATCAATTAATGCGTCGTAATGCTCGTCAAGCATACGCTGTTAGCGCTGAAGCA
GGCCATCAAACATCAGCTGAATCATGGGGTACAGGTCGTGCTGTTGCTCGTATTCCTCGA
GTTCGTGGTGGTGGTACTCATCGTTCAGGTCAGGGTGCTTTCGGAAATATGTGTCGTGGA
GGTCGCATGTTCGCTCCAACTAAACCATGGCGTAGATGGCATCGTCGCATTAATGTCAAC
TTGAAACGTTATGCAGTTGTTTCAGCTGTTGCTGCATCAGGCGTTCCAGCTCTTGTTCAA
GCTCGAGGTATATTTAAATAATCTAAAAAAGGATTATGTTCTAATAATATTTAATTTTAG
GACATATTATTGACGGTTTATCGTTCAAAACGCTTTAGAGCTGGTCGTGGTAAAATGCGA
AATCGTCGTCGTATTCAACGTCGTGGACCATTAATTGTTTACTCGAAGGATGATGGCTTG
CGTCGTGCATTCCGTAATATTCCCGGTGTTGATACAATGAGCGTTCACAAATTGAATTTG
CTCAAATTGGCTCCAGGTGGACATCTTGGACGATTGATTGTTTGGACCGAAGGCGCTTTC
AAGCATTTGAATGCATTGTTTGGAACATGGAGTGAGCCTTCAACAGTGAAAAAGGCTTAC
AATCTGCCACATCCAATTATGTCTAACACTGATTTGACTCGCTTGCTCAAATCACAAGAA
ATCAAGAGCGTTTTGAATGCACCTAAGAAGAGAGTTTTCCATCGTGTACGCCGCTTGAAT
CCATTGAAGAACGCCAGACAAAAGACCAACGAAAGTATGAGACACAAATTGCCAAGGCAA
AGAAGAAGAAGGTCGAACTCAAGAGCAATCATCCAGCTATTGTGTATCAAAAGAATGTTG
CTAATCGTTTGAAGCTCTTAGCTGCATCAAAGAAAGCTAGACAAGCTCGCGCTGCTGAAA
AGAAAAAAGCTGCTGCTGGAAAGAAAGCAACAAAAAAGACCGCAGCCAAGAAAAAGTAA
>g3343.t54 Gene=g3343 Length=101
MRRNARQAYAVSAEAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFA
PTKPWRRWHRRINVNLKRYAVVSAVAASGVPALVQARGIFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3343.t54 | Gene3D | G3DSA:3.40.1370.10 | - | 1 | 100 | 2.2E-42 |
| 5 | g3343.t54 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 28 | - |
| 2 | g3343.t54 | PANTHER | PTHR19431 | 60S RIBOSOMAL PROTEIN L4 | 3 | 98 | 6.1E-53 |
| 3 | g3343.t54 | PANTHER | PTHR19431:SF6 | BNAC03G35890D PROTEIN | 3 | 98 | 6.1E-53 |
| 1 | g3343.t54 | Pfam | PF00573 | Ribosomal protein L4/L1 family | 2 | 98 | 4.0E-13 |
| 7 | g3343.t54 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 78 | - |
| 9 | g3343.t54 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 79 | 100 | - |
| 8 | g3343.t54 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 101 | 101 | - |
| 4 | g3343.t54 | SUPERFAMILY | SSF52166 | Ribosomal protein L4 | 2 | 98 | 1.57E-28 |
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. There were no conditions that were differentially expressed