General information for g534.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ubiquitin-protein ligase E3C.
Parent gene
- The parent gene g534 is located on chr_3: 3967847..3968996 (+ 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 | g534 | g534.t2 | TSS | g534.t2 | 3965392 | 3965392 |
| chr_3 | g534 | g534.t2 | isoform | g534.t2 | 3965428 | 3966294 |
| chr_3 | g534 | g534.t2 | exon | g534.t2.exon1 | 3965428 | 3965597 |
| chr_3 | g534 | g534.t2 | cds | g534.t2.CDS1 | 3965428 | 3965597 |
| chr_3 | g534 | g534.t2 | exon | g534.t2.exon2 | 3965659 | 3965809 |
| chr_3 | g534 | g534.t2 | cds | g534.t2.CDS2 | 3965659 | 3965809 |
| chr_3 | g534 | g534.t2 | exon | g534.t2.exon3 | 3965867 | 3966294 |
| chr_3 | g534 | g534.t2 | cds | g534.t2.CDS3 | 3965867 | 3966292 |
| chr_3 | g534 | g534.t2 | TTS | g534.t2 | 3967062 | 3967062 |
Sequences
>g534.t2 Gene=g534 Length=749
ATGTTTAATTTTGACGGAAATTTTCGTCGTTTGCCAGTTCAATCGCTTGGAGGATCATCT
ATAGAAACAGATCGTAGTCGTTTAATCAAAAAAGCACAAGATGAGCGTAAGAAACGGGAA
GAATTGAGAAAAAAGGAAATTTCCTGCATTACAATTCAAAAGTGGATTAGGAGTTTTCAT
CAACGACAGGCTGTCAAACGACGAGAACGACTTAATTATGAAAGTTATATAAAAACGAAT
GGCTTAAAGAATATTCAAGATCTTGAATTTTTGCTAAAACGACTGCTGTATTACTATGAC
TTGAATGATAGTGATAAACTTATTACATTATGCCAATTTATAATCAAAAATGTTGGCATA
CTATTTGAAATAATCCTTCAAAACAATAATAGTTTTATTAAACAAAAATTACAATGGCAA
TTTCGCATACAAAAACTATTGACTCTATGTCTTAAACAAATATTTGTGTCACCATCAACA
TCAATAGCAATCCCAATGAGAACAATTGAAATTTTCACTTCTTTTGAATCAATAAGAAAT
TTTGCACCGGCTGGCATTAATGAGAATGACCTCATGAAATTCTCACGTCAAATTTTCTCT
TACATGATTGATCAAAATTACTATGAAAATGTACGAAAGATGTTGAATGAGAAAATTGCT
GAAAATACGTACGATGAAATCACAACTGTGCCGCGCACTGAAATCTCAAAAGTAATTCTG
TCAATGATTGAACGACCATTAAAATTGGT
>g534.t2 Gene=g534 Length=249
MFNFDGNFRRLPVQSLGGSSIETDRSRLIKKAQDERKKREELRKKEISCITIQKWIRSFH
QRQAVKRRERLNYESYIKTNGLKNIQDLEFLLKRLLYYYDLNDSDKLITLCQFIIKNVGI
LFEIILQNNNSFIKQKLQWQFRIQKLLTLCLKQIFVSPSTSIAIPMRTIEIFTSFESIRN
FAPAGINENDLMKFSRQIFSYMIDQNYYENVRKMLNEKIAENTYDEITTVPRTEISKVIL
SMIERPLKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g534.t2 | Coils | Coil | Coil | 25 | 45 | - |
| 1 | g534.t2 | PANTHER | PTHR45700:SF2 | UBIQUITIN-PROTEIN LIGASE E3C | 2 | 248 | 1.8E-19 |
| 2 | g534.t2 | PANTHER | PTHR45700 | UBIQUITIN-PROTEIN LIGASE E3C | 2 | 248 | 1.8E-19 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g534/g534.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g534.t2.fa.iupred3.txt does not exist
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