General information for g5712.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L28, mitochondrial.
Parent gene
- The parent gene g5712 is located on chr_2: 11340809..11341769 (+ 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 | g5712 | g5712.t4 | TSS | g5712.t4 | 11340726 | 11340726 |
| chr_2 | g5712 | g5712.t4 | isoform | g5712.t4 | 11340809 | 11341769 |
| chr_2 | g5712 | g5712.t4 | exon | g5712.t4.exon1 | 11340809 | 11340884 |
| chr_2 | g5712 | g5712.t4 | cds | g5712.t4.CDS1 | 11340809 | 11340884 |
| chr_2 | g5712 | g5712.t4 | exon | g5712.t4.exon2 | 11340951 | 11341663 |
| chr_2 | g5712 | g5712.t4 | cds | g5712.t4.CDS2 | 11340951 | 11341663 |
| chr_2 | g5712 | g5712.t4 | exon | g5712.t4.exon3 | 11341718 | 11341769 |
| chr_2 | g5712 | g5712.t4 | TTS | g5712.t4 | 11341814 | 11341814 |
Sequences
>g5712.t4 Gene=g5712 Length=841
ATGGCATCTTCAGTTAAGCAAGGATTTGCCACACTCAAAAAAGTTCATGTTAATAAGCGT
TTTTCGGTTGGATTAGGAGCACAAGTTCCTGAGGCTTATAGAAAATTTTGGGCTGAATGG
ATGGAAAGGCAGCCAGCTGCAGTGCATTATATACCAAATGAAGGCAGATTTAAACGCAAT
CAGAAAACTGGTGAAGTAGTTCCGATTCAAAATGTTCATATTCCTTTAAAGAGAGTTGTT
GAAGAGAATTTTGGAATATGGGGAGGTGAAGCAGTAATTCAAGGTTTTAAAAAGCCTGAA
ATGAAACATCGAAAGCCATGTTTCTGGGTGCCAACATTAAAACGTTCTGCAGTTCGTAGT
GAAGTACTCAATGAATTTTTCTCTGTAACTTTGACTGATCGTACAATAACTCTAATTCAT
GAACATCATGGCTTTGATCATTATTTGTTAAAATCACCAGCATGTGATTTGAGATCCGTT
TTAGCATTGAAAATTAAGAGAAAAATTCTAATTGATTTACTTAATGGATGCCCAGCATGG
GACCATAACAAAACAAGGCAAGACGAAGTGAAGAAAGAGTTTTCTCAATATTTGGAACAA
TACACACCGGAAGAAATTGAGTGGTACGGATTGACTTATGCTGAAGCATTGGCAAAAACT
CAAAAAATGATCAAGGAAGCAAATCCAATAGTTCCTCATAAACAAATTTTCCGTGAGAAA
CTCATTGAACAACTTAAACAAGCTGGTTTGGAAGAAGTCACAGGAGAGAAAGCTGCAGAT
GAAGAGTAAAAGTTCTTGGCTGAAAAAACTCAATCCATTTTCAAAGAAGAAAGAATTCTA
A
>g5712.t4 Gene=g5712 Length=262
MASSVKQGFATLKKVHVNKRFSVGLGAQVPEAYRKFWAEWMERQPAAVHYIPNEGRFKRN
QKTGEVVPIQNVHIPLKRVVEENFGIWGGEAVIQGFKKPEMKHRKPCFWVPTLKRSAVRS
EVLNEFFSVTLTDRTITLIHEHHGFDHYLLKSPACDLRSVLALKIKRKILIDLLNGCPAW
DHNKTRQDEVKKEFSQYLEQYTPEEIEWYGLTYAEALAKTQKMIKEANPIVPHKQIFREK
LIEQLKQAGLEEVTGEKAADEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5712.t4 | Gene3D | G3DSA:2.30.170.40 | Ribosomal protein L34p | 50 | 175 | 0 |
| 1 | g5712.t4 | PANTHER | PTHR13528:SF2 | 39S RIBOSOMAL PROTEIN L28, MITOCHONDRIAL | 20 | 246 | 0 |
| 2 | g5712.t4 | PANTHER | PTHR13528 | 39S RIBOSOMAL PROTEIN L28, MITOCHONDRIAL | 20 | 246 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5712/g5712.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5712.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02902 (large subunit ribosomal protein L28)
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.
