General information for g3900.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3900 is located on chr_3: 28718171..28720063 (- 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 | g3900 | g3900.t4 | TTS | g3900.t4 | 28715266 | 28715266 |
| chr_3 | g3900 | g3900.t4 | isoform | g3900.t4 | 28715338 | 28716145 |
| chr_3 | g3900 | g3900.t4 | exon | g3900.t4.exon1 | 28715338 | 28715526 |
| chr_3 | g3900 | g3900.t4 | cds | g3900.t4.CDS1 | 28715338 | 28715526 |
| chr_3 | g3900 | g3900.t4 | exon | g3900.t4.exon2 | 28715584 | 28715753 |
| chr_3 | g3900 | g3900.t4 | cds | g3900.t4.CDS2 | 28715584 | 28715753 |
| chr_3 | g3900 | g3900.t4 | exon | g3900.t4.exon3 | 28715844 | 28715938 |
| chr_3 | g3900 | g3900.t4 | cds | g3900.t4.CDS3 | 28715844 | 28715938 |
| chr_3 | g3900 | g3900.t4 | exon | g3900.t4.exon4 | 28716009 | 28716145 |
| chr_3 | g3900 | g3900.t4 | cds | g3900.t4.CDS4 | 28716009 | 28716043 |
| chr_3 | g3900 | g3900.t4 | TSS | g3900.t4 | NA | NA |
Sequences
>g3900.t4 Gene=g3900 Length=591
AGTATCAAACAGTCTTACAAACTAATCCAGATGGAACATTCTCATTAATTCAAGTTGATC
CAAGTACATTATCAAATAATCCATCGATAATCACTTTACCTGATGGTACAACAGCTCAAG
TTCAAGGTGTTGCTACTACAAAGTGATGGCACAACTGTCCATACAGTCCAAGCTCTTGAT
GGTCAAACAGAAAATATGCAAGTAGATCTCTCAGAAGCTCTTGCTCAAGATGGCCCATAT
CCAGTGTTTGTTTCTCTACCAGTTACCGCACAAATGTATCATTCACTCGTGCAGCAACAA
ATTCCAAATTCTGACAATACAGTTTGTGTGACTCCTATGCAGGTACAAAATTTCATTACA
AGTAATAGTTTATGTTGTGCTAGTATTACAAATCAAAATTCTTTTCAAACAACATCAGCA
ACAAATTGTCATATAAAGTCCGTTCTCGCTAATCCAAAGGCATCGAAAATTCGAACAGCG
GTTATTAAAAAGCCACTGATTAAAAAACAGCGAATACTAAATGTGGCGGTCGCTAAAGTA
AAACCAAAAATTGATAACATTAAAGTGATTAGTGGCACCATTAGCCACACT
>g3900.t4 Gene=g3900 Length=163
MVQQLKFKVLLLQSDGTTVHTVQALDGQTENMQVDLSEALAQDGPYPVFVSLPVTAQMYH
SLVQQQIPNSDNTVCVTPMQVQNFITSNSLCCASITNQNSFQTTSATNCHIKSVLANPKA
SKIRTAVIKKPLIKKQRILNVAVAKVKPKIDNIKVISGTISHT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g3900.t4 | Pfam | PF10492 | Nrf1 activator activation site binding domain | 50 | 130 | 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.
