General information for g5828.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative E3 ubiquitin-protein ligase MIB2.
Parent gene
- The parent gene g5828 is located on chr_2: 12103796..12112762 (+ 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 | g5828 | g5828.t3 | isoform | g5828.t3 | 12103796 | 12110059 |
| chr_2 | g5828 | g5828.t3 | exon | g5828.t3.exon1 | 12103796 | 12104249 |
| chr_2 | g5828 | g5828.t3 | TSS | g5828.t3 | 12103797 | 12103797 |
| chr_2 | g5828 | g5828.t3 | exon | g5828.t3.exon2 | 12108656 | 12108758 |
| chr_2 | g5828 | g5828.t3 | exon | g5828.t3.exon3 | 12108821 | 12109057 |
| chr_2 | g5828 | g5828.t3 | exon | g5828.t3.exon4 | 12109155 | 12109235 |
| chr_2 | g5828 | g5828.t3 | exon | g5828.t3.exon5 | 12109539 | 12109678 |
| chr_2 | g5828 | g5828.t3 | cds | g5828.t3.CDS1 | 12109591 | 12109678 |
| chr_2 | g5828 | g5828.t3 | exon | g5828.t3.exon6 | 12109783 | 12110059 |
| chr_2 | g5828 | g5828.t3 | cds | g5828.t3.CDS2 | 12109783 | 12110057 |
| chr_2 | g5828 | g5828.t3 | TTS | g5828.t3 | NA | NA |
Sequences
>g5828.t3 Gene=g5828 Length=1292
TTAGTACTATTTTGTAGATCTCCGATTAAAGACGTGTGTGCGGCTGTAGCAAAGCAGCAG
CGTGTAGCAAAAAAAGAAACATAAATCAGCCGTTTTAAAAAGAAATTTCTTCTCTCGCTC
TATCGATTTGCGGAAAAGTTTAATTTTCATGTGAGAAGAAGGCAAAAAAAAAACTTTCGT
TTTCTTCTTTTGTGCTACGAAAACTAAAGAACAATTTTTTATTTGTGCTGTTTCTGTTGT
TTGTTATTTTTTTCTTCTTCTTATTATTCAATTTTGAGTGCAATGAATTATTTCAAGTAT
CATTGAAAATTGGTTGGAAATATCGGAAAAAAACATTTTTGTACTTAATTTGAAGACAAA
GCCTGTGAAATTTTTTTTGAATTTTTATTTATTGATTATTGAAAAAATTGATTGTGTGAC
TTACAATAGATAGAATCAAAATAATAAAAGAAATACGGAGGTGAAGGTCACGTTGGAACA
CTTTGTGAAGTTGGCCGGTCAGGTTCCACACATTCACCAGAGAAAACAGTTGTTGTTAAT
TGGGACTCGGGTCATCGAACAAATTATCGTGTAGGCTATCAATGTCAGTATGATCTTATA
GTTGTTGACAACGCTCAAATTGGCGTGCGTCATCCAAATATAATTTGTGACGGTTGTAAA
AAAGCAGGAATTGCTGGAATTCTCTTCCGCTGTGCAGAATGTGCCAATTTTGATTTATGT
GCTCATTGCTATGGAAATGATGTTCACAATTTAGAGCATTCCTTTGTGCGCTATCAGACG
GCAAACTCTGTTGGTGTTCGTGTACCTCCACGTGCTGGCTCAGTTCGTATACAACTCAAA
GGAATTTTCGTTAACGCAAAAGTTGTTCGTGGACCCGATTGGGAGTGGGGTCAACAAGAT
GGTGGCGAAGGCAAGACAGGTCGAGTGATGGAAATTCGTGGATGGGACAATGAATCATGT
CGAAGTGTTGCGAATGTTTCATGGGCATCTGGTTCCACTAATGTTTATAGATTAGGTCAT
AAAGGTAACGTTGATTTAAAATACGTTGTGCCAGCTGTGGGCGGTTATTATTACAAGGAT
CACATGCCTGTGTTAGGGCAACGTGACGAACAGCAGCCCGTCATTCAGGCTACACGACCA
ATTTTCTATGTTGGTGATCGTGTGCGTGTATGTTTGGATAAAGAAAGTCTTATGAGGCTG
CAATCGGGTCATGGTGGTTGGAATCCAAGAATGGCTGAATTTCTCAGCAAAATTGGAACT
GTTCATCGGATTACTGAAAAAGGTGATATTAG
>g5828.t3 Gene=g5828 Length=121
MEIRGWDNESCRSVANVSWASGSTNVYRLGHKGNVDLKYVVPAVGGYYYKDHMPVLGQRD
EQQPVIQATRPIFYVGDRVRVCLDKESLMRLQSGHGGWNPRMAEFLSKIGTVHRITEKGD
I
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5828.t3 | Gene3D | G3DSA:2.30.30.920 | - | 3 | 46 | 0.0000002 |
| 3 | g5828.t3 | PANTHER | PTHR24202 | - | 2 | 121 | 0.0000000 |
| 1 | g5828.t3 | Pfam | PF06701 | Mib_herc2 | 2 | 40 | 0.0000000 |
| 2 | g5828.t3 | Pfam | PF18346 | Mind bomb SH3 repeat domain | 73 | 121 | 0.0000000 |
| 6 | g5828.t3 | ProSiteProfiles | PS51416 | MIB/HERC2 domain profile. | 1 | 43 | 14.5680000 |
| 4 | g5828.t3 | SUPERFAMILY | SSF159034 | Mib/herc2 domain-like | 14 | 40 | 0.0000055 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5828/g5828.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5828.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0046872 | metal ion binding | MF |
| GO:0016567 | protein ubiquitination | BP |
| GO:0004842 | ubiquitin-protein transferase activity | 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.
