General information for g3458.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein purity of essence.
Parent gene
- The parent gene g3458 is located on chr_3: 25550178..25552827 (+ 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 | g3458 | g3458.t5 | isoform | g3458.t5 | 25550178 | 25552827 |
| chr_3 | g3458 | g3458.t5 | exon | g3458.t5.exon1 | 25550178 | 25551083 |
| chr_3 | g3458 | g3458.t5 | cds | g3458.t5.CDS1 | 25550260 | 25550967 |
| chr_3 | g3458 | g3458.t5 | exon | g3458.t5.exon2 | 25552654 | 25552827 |
| chr_3 | g3458 | g3458.t5 | TSS | g3458.t5 | NA | NA |
| chr_3 | g3458 | g3458.t5 | TTS | g3458.t5 | NA | NA |
Sequences
>g3458.t5 Gene=g3458 Length=1080
TCTTCAAAATACAAATACAAAGTGCAACGGTTTATTGCCATTATGGGGTCCAGATGTTAG
TGAAACTGCATTCAGTGCTTGTATGGCTCGTCAGCATAGCTATTTACAAGACAGCACTCA
ACGAATTGACATTACTTTTGCAAGTGGAATTCATGATTTGAAATTATTGTTATTGAGATT
TGCTCACGAAAAAACTTTTCACGATGATTGTAGTGGTGGTGGTCCACAATCAAATATGCA
CTTGGTTCCATATTTAATGTTTTTTTCACTTTACATCTCATTATCAACTCGATCATATAC
GCGTGAAGAGAAAGCATTGACAACTTTCTTGAATCAACCAGTAGGAGAGAAATGGCTAGA
ATCGTCTTATGAAGTTGATGGATCAGTATATCAAACAGTTTTGAGCATTGTTTTACATAC
ACCTGAAATGTGGTCAAAAAATCGAATCAAATATCTTAAAAGATTAATTGTCACCTATCA
TGTGCGACATTTATATCCATCATCAACCTGCAAAGCACTTAACGGAGTTGGCGATAAAGA
TATAAAGGACTATAGTGTTTACAAGGGTGGTCTTATGATTTTTGCTCTAGTAGAACTCAT
TTACAAATATTTTTTCGCAAAAGTTGTTAATCCAAAAGACGAAGATTGGTCTGTGTCACT
TTTCAATTATATTCGAAAGAATGACGAAGCAATGCTAAAATCAGCTGTTACTGTTTTGGA
AAATTTCCGCGACGAATATTTGCCATGTACATCGTTTGGTGAATTTTGTGATGTTGCCGG
TAAGTGTTGATGTTTTGTTTTTTTATATTCTAGTTTTTCTAATCTTTTTTTGTTTTATAA
CAGGTCTCTTGGATGAAATTGATGATCCAGATAAATTCTTATTGGACCTCTTGCAGTCGT
TGCCCTACATCGCTTATTGATACAGTTGTTTTACACGCCTATTGGAGCATACACTCAAAA
AAATTATTGAATAATATTTATAATCATGTGTCGATTTTGAGTGATTGAATGTGTGTTGAA
AGAAAGAAAAAATAAGTTGATAAATGTCGCGATTATCTAAATAACTAAATGAGTGTCACT
>g3458.t5 Gene=g3458 Length=235
MARQHSYLQDSTQRIDITFASGIHDLKLLLLRFAHEKTFHDDCSGGGPQSNMHLVPYLMF
FSLYISLSTRSYTREEKALTTFLNQPVGEKWLESSYEVDGSVYQTVLSIVLHTPEMWSKN
RIKYLKRLIVTYHVRHLYPSSTCKALNGVGDKDIKDYSVYKGGLMIFALVELIYKYFFAK
VVNPKDEDWSVSLFNYIRKNDEAMLKSAVTVLENFRDEYLPCTSFGEFCDVAGKC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3458.t5 | PANTHER | PTHR21725:SF1 | E3 UBIQUITIN-PROTEIN LIGASE UBR4 | 2 | 233 | 0 |
| 3 | g3458.t5 | PANTHER | PTHR21725 | E3 UBIQUITIN-PROTEIN LIGASE UBR4 | 2 | 233 | 0 |
| 1 | g3458.t5 | Pfam | PF13764 | E3 ubiquitin-protein ligase UBR4 | 2 | 233 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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