General information for g3343.t2
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.t2 | isoform | g3343.t2 | 24744170 | 24754773 |
| chr_3 | g3343 | g3343.t2 | exon | g3343.t2.exon1 | 24744170 | 24744213 |
| chr_3 | g3343 | g3343.t2 | exon | g3343.t2.exon2 | 24752889 | 24753703 |
| chr_3 | g3343 | g3343.t2 | cds | g3343.t2.CDS1 | 24753005 | 24753703 |
| chr_3 | g3343 | g3343.t2 | exon | g3343.t2.exon3 | 24753929 | 24754053 |
| chr_3 | g3343 | g3343.t2 | cds | g3343.t2.CDS2 | 24753929 | 24754053 |
| chr_3 | g3343 | g3343.t2 | exon | g3343.t2.exon4 | 24754107 | 24754533 |
| chr_3 | g3343 | g3343.t2 | cds | g3343.t2.CDS3 | 24754107 | 24754533 |
| chr_3 | g3343 | g3343.t2 | exon | g3343.t2.exon5 | 24754771 | 24754773 |
| chr_3 | g3343 | g3343.t2 | cds | g3343.t2.CDS4 | 24754771 | 24754773 |
| chr_3 | g3343 | g3343.t2 | TSS | g3343.t2 | 24754851 | 24754851 |
| chr_3 | g3343 | g3343.t2 | TTS | g3343.t2 | NA | NA |
Sequences
>g3343.t2 Gene=g3343 Length=1414
ATGAGTAAATCAGCTGCTCGTCCGCTCGTCAGTGTTTATACTGACAAAAGTGAGGTTATT
AAAGATACAACAATTCCATTGCCTGCAATTTTCAAGGCTCCAATTCGCCCAGATGTCGTC
AATGATGTACATCAATTAATGCGTCGTAATGCTCGTCAAGCATACGCTGTTAGCGCTGAA
GCAGGCCATCAAACATCAGCTGAATCATGGGGTACAGGTCGTGCTGTTGCTCGTATTCCT
CGAGTTCGTGGTGGTGGTACTCATCGTTCAGGTCAGGGTGCTTTCGGAAATATGTGTCGT
GGAGGTCGCATGTTCGCTCCAACTAAACCATGGCGTAGATGGCATCGTCGCATTAATGTC
AACTTGAAACGTTATGCAGTTGTTTCAGCTGTTGCTGCATCAGGCGTTCCAGCTCTTGTT
CAAGCTCGAGGACATATTATTGACGGAATTGCTGAACTTCCATTGGTTGTCTCAGATAAA
GTTCAAGAATACAACAAGACCAAACAAGCTGTTTTGTTCTTACGTCGTAACAAGTTGTGG
GGAGATGTTTTGAAAGTTTATCGTTCAAAACGCTTTAGAGCTGGTCGTGGTAAAATGCGA
AATCGTCGTCGTATTCAACGTCGTGGACCATTAATTGTTTACTCGAAGGATGATGGCTTG
CGTCGTGCATTCCGTAATATTCCCGGTGTTGATACAATGAGCGTTCACAAATTGAATTTG
CTCAAATTGGCTCCAGGTGGACATCTTGGACGATTGATTGTTTGGACCGAAGGCGCTTTC
AAGCATTTGAATGCATTGTTTGGAACATGGAGTGAGCCTTCAACAGTGAAAAAGGCTTAC
AATCTGCCACATCCAATTATGTCTAACACTGATTTGACTCGCTTGCTCAAATCACAAGAA
ATCAAGAGCGTTTTGAATGCACCTAAGAAGAGAGTTTTCCATCGTGTACGCCGCTTGAAT
CCATTGAAGAACGCCAGACAAAAGACCAAGTTGAATCCATATTCAGAAGTTACTCGTCGT
CGTGCATTGTTGGCTAAAGAAAAGCGAAAGTATGAGACACAAATTGCCAAGGCAAAGAAG
AAGAAGGTCGAACTCAAGAGCAATCATCCAGCTATTGTGTATCAAAAGAATGTTGCTAAT
CGTTTGAAGCTCTTAGCTGCATCAAAGAAAGCTAGACAAGCTCGCGCTGCTGAAAAGAAA
AAAGCTGCTGCTGGAAAGAAAGCAACAAAAAAGACCGCAGCCAAGAAAAAGTAAATTATA
AATTTGATGGTAAATACACATATTAAAGAATTCGAGAAATGTAATCATGTTGTACACCAT
ATAATGACGAATTCTGAAAGTTTATAATAAAAATAAAACATGAATCAAAAAAAAAAACTG
TTTCAATTACGAGTGTAATTGAAAAAAAGAAAAA
>g3343.t2 Gene=g3343 Length=417
MSKSAARPLVSVYTDKSEVIKDTTIPLPAIFKAPIRPDVVNDVHQLMRRNARQAYAVSAE
AGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKPWRRWHRRINV
NLKRYAVVSAVAASGVPALVQARGHIIDGIAELPLVVSDKVQEYNKTKQAVLFLRRNKLW
GDVLKVYRSKRFRAGRGKMRNRRRIQRRGPLIVYSKDDGLRRAFRNIPGVDTMSVHKLNL
LKLAPGGHLGRLIVWTEGAFKHLNALFGTWSEPSTVKKAYNLPHPIMSNTDLTRLLKSQE
IKSVLNAPKKRVFHRVRRLNPLKNARQKTKLNPYSEVTRRRALLAKEKRKYETQIAKAKK
KKVELKSNHPAIVYQKNVANRLKLLAASKKARQARAAEKKKAAAGKKATKKTAAKKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3343.t2 | Coils | Coil | Coil | 341 | 368 | - |
| 8 | g3343.t2 | Gene3D | G3DSA:3.40.1370.10 | - | 4 | 307 | 4.5E-134 |
| 7 | g3343.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 389 | 417 | - |
| 3 | g3343.t2 | PANTHER | PTHR19431 | 60S RIBOSOMAL PROTEIN L4 | 4 | 397 | 7.2E-170 |
| 4 | g3343.t2 | PANTHER | PTHR19431:SF0 | 60S RIBOSOMAL PROTEIN L4 | 4 | 397 | 7.2E-170 |
| 1 | g3343.t2 | Pfam | PF00573 | Ribosomal protein L4/L1 family | 25 | 264 | 2.3E-39 |
| 2 | g3343.t2 | Pfam | PF14374 | 60S ribosomal protein L4 C-terminal domain | 278 | 350 | 1.4E-23 |
| 6 | g3343.t2 | ProSitePatterns | PS00939 | Ribosomal protein L1e signature. | 119 | 145 | - |
| 5 | g3343.t2 | SUPERFAMILY | SSF52166 | Ribosomal protein L4 | 9 | 264 | 3.14E-81 |
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 K02930 (large subunit ribosomal protein L4e)
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.
