General information for g5932.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L31.
Parent gene
- The parent gene g5932 is located on chr_2: 12895340..12895485 (+ 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 | g5932 | g5932.t1 | isoform | g5932.t1 | 12893950 | 12895485 |
| chr_2 | g5932 | g5932.t1 | exon | g5932.t1.exon1 | 12893950 | 12893960 |
| chr_2 | g5932 | g5932.t1 | cds | g5932.t1.CDS1 | 12893950 | 12893960 |
| chr_2 | g5932 | g5932.t1 | exon | g5932.t1.exon2 | 12894641 | 12894677 |
| chr_2 | g5932 | g5932.t1 | cds | g5932.t1.CDS2 | 12894641 | 12894677 |
| chr_2 | g5932 | g5932.t1 | exon | g5932.t1.exon3 | 12895045 | 12895274 |
| chr_2 | g5932 | g5932.t1 | cds | g5932.t1.CDS3 | 12895045 | 12895274 |
| chr_2 | g5932 | g5932.t1 | exon | g5932.t1.exon4 | 12895338 | 12895485 |
| chr_2 | g5932 | g5932.t1 | cds | g5932.t1.CDS4 | 12895338 | 12895485 |
| chr_2 | g5932 | g5932.t1 | TTS | g5932.t1 | 12895626 | 12895626 |
| chr_2 | g5932 | g5932.t1 | TSS | g5932.t1 | NA | NA |
Sequences
>g5932.t1 Gene=g5932 Length=426
ATGGATTTGATAACTCTTTCTTTTTTCTCTAACAAACTCACACGTTTGATAGAAATGGCG
AAGGGTAAAACAGAAAAGCGTACCAAATCGGCAATCAATGAAGTTGTGACACGAGAGTGC
ACAATTCATCTGAATAAGCGACTCCACAAAGTTGGTTTTAAAAAACGTTCACCAAGAGCA
GTTAAGATCATTCGTAAATTTGCTGAAAAGGAAATGGGAACAAAAGATGTGAGAATTGAT
ACCCGTCTTAATAAAGCAATTTGGTCTCGCGGTATCAGAAATCCACCTTTCCGCATTCGT
GTTCGACTTGCTCGCCGCCGTAATGATGATGAAGATTCACCTAACAAGCTTTATACTTTG
GTCACATACGTCCCAGTGGAAAGCTTCAAAGAACTCCAAACAGAAAATGTTGAATCAGAA
GATTAA
>g5932.t1 Gene=g5932 Length=141
MDLITLSFFSNKLTRLIEMAKGKTEKRTKSAINEVVTRECTIHLNKRLHKVGFKKRSPRA
VKIIRKFAEKEMGTKDVRIDTRLNKAIWSRGIRNPPFRIRVRLARRRNDDEDSPNKLYTL
VTYVPVESFKELQTENVESED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5932.t1 | CDD | cd00463 | Ribosomal_L31e | 32 | 115 | 1.49097E-28 |
| 6 | g5932.t1 | Gene3D | G3DSA:3.10.440.10 | - | 19 | 140 | 2.6E-56 |
| 4 | g5932.t1 | Hamap | MF_00410 | 50S ribosomal protein L31e [rpl31e]. | 33 | 127 | 15.773115 |
| 2 | g5932.t1 | PANTHER | PTHR10956:SF4 | 60S RIBOSOMAL PROTEIN L31 | 20 | 139 | 2.1E-55 |
| 3 | g5932.t1 | PANTHER | PTHR10956 | 60S RIBOSOMAL PROTEIN L31 | 20 | 139 | 2.1E-55 |
| 1 | g5932.t1 | Pfam | PF01198 | Ribosomal protein L31e | 34 | 115 | 1.4E-43 |
| 8 | g5932.t1 | ProSitePatterns | PS01144 | Ribosomal protein L31e signature. | 77 | 91 | - |
| 9 | g5932.t1 | SMART | SM01380 | Ribosomal_L31e_2 | 33 | 116 | 1.8E-54 |
| 5 | g5932.t1 | SUPERFAMILY | SSF54575 | Ribosomal protein L31e | 34 | 116 | 2.62E-34 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5932/g5932.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5932.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 K02910 (large subunit ribosomal protein L31e)
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. There were no conditions that were differentially expressed