General information for g3900.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA-binding protein Ewg.
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.t3 | TTS | g3900.t3 | 28714001 | 28714001 |
| chr_3 | g3900 | g3900.t3 | isoform | g3900.t3 | 28714671 | 28718174 |
| chr_3 | g3900 | g3900.t3 | exon | g3900.t3.exon1 | 28714671 | 28715753 |
| chr_3 | g3900 | g3900.t3 | cds | g3900.t3.CDS1 | 28715173 | 28715753 |
| chr_3 | g3900 | g3900.t3 | exon | g3900.t3.exon2 | 28715811 | 28715946 |
| chr_3 | g3900 | g3900.t3 | cds | g3900.t3.CDS2 | 28715811 | 28715946 |
| chr_3 | g3900 | g3900.t3 | exon | g3900.t3.exon3 | 28716009 | 28716143 |
| chr_3 | g3900 | g3900.t3 | cds | g3900.t3.CDS3 | 28716009 | 28716143 |
| chr_3 | g3900 | g3900.t3 | exon | g3900.t3.exon4 | 28717933 | 28718174 |
| chr_3 | g3900 | g3900.t3 | cds | g3900.t3.CDS4 | 28717933 | 28718094 |
| chr_3 | g3900 | g3900.t3 | TSS | g3900.t3 | NA | NA |
Sequences
>g3900.t3 Gene=g3900 Length=1596
GACGAGGTAAACCAGGTTGGGGCCGTGATTCCACGCGGCCAGAATGGTGGCCTAAAGAAC
TTCCATGGGCAAATGTGAGAATGGACGCACGAACAGAAGAAGAAAAACAAAAAATTAGCT
GGACACATGCATTGCGAAAAATTGTTATAAACTGTTACAAATATCATGGACGAGAAGACT
TATTACCAGCATTCTCTGAAGAAGATGAAAAAGCAAATGCAATCGCAACTGCCAATGCAA
ATTATCAAACAGTCTTACAAACTAATCCAGATGGAACATTCTCATTAATTCAAGTTGATC
CAAGTACATTATCAAATAATCCATCGATAATCACTTTACCTGATGGTACAACAGCTCAAG
TTCAAGGTGTTGCTACTTTGCATACACAAAGTGATGGCACAACTGTCCATACAGTCCAAG
CTCTTGATGGTCAAACAGAAAATATGCAAGTAGATCTCTCAGAAGCTCTTGCTCAAGATG
GTCAACTAATAATCACAAATGAAGATGGAAATGGCCCATATCCAGTGTTTGTTTCTCTAC
CAGTTACCGCACAAATGTATCATTCACTCGTGCAGCAACAAATTCCAAATTCTGACAATA
CAGTTTGTGTGACTCCTATGCAGGTACAAAATTTCATTACAAGTAATAGTTTATGTTGTG
CTAGTATTACAAATCAAAATTCTACAACATATTTAATGGCGGCAAATAATAATGGTTCCA
AGAATGTTGTAAACTTGCCTTTTCAAACAACATCAGCAACAAATTGTCATATAAAGTCCG
TTCTCGCTAATCCAAAGGCATCGAAAATTCGAACAGCGGTTATTAAAAAGCCACTGATTA
AAAAACAGCGAATACTAAATGTGGCGGTCGCTAAAGTAAAACCAAAAATTGATAACATTA
AAGTGATTAGTGGCACCATTAGCCACACTGATAATAACAATACCAAAAAAGTCAAAGATA
AAAATGAAAAATTATCCCAAGAAGATATAAAAATTTTACCGAAAAAAAGTAAAAATATAC
AAACCAAAGTTTCATTAAAGCATATTGAGTTGAAACTGAAGAAAGAAAGTTCTTTAGAGA
AAAAACAAGAGTAGTCATTAGATGATAGGAAGTACAAGAATTAAATTTTTATTTTATTTT
AAAATTGGATAATTTTTCCTCCAATTTGTTTTAATGATCTCTCATTTGACCATTGTAATA
TTAAATTAAGAATAAGAGTCATAATTTATGTGCCTTATAGTATAAACCACAATTATGAAT
ACAAAAATAATACACAAAAATAATTCACAAATCATAATGAAAAATGATGATTATTGTGAA
TAGATAAAAAAAATTTAGTCAACAATTATGGTTTGACAGTTCCTTAAGCATACTACGTTA
GTCATAAATATGAATGTACTATTTAAAAAAATTTTTAGTCATAACTTCGTTGATAAAATG
AACAGTTTTGAAAATTTCAATGCTTTGAAAGCACTGCAAAATTGTTACCACCAGGAATTA
AATATCCCTAAATCATATTGAACAAAAAATAAAAACTTTAGATTATTATTTTATGTTGAA
ACTTTTAATTTATATAATTTATTAGGGTTTGTAAAA
>g3900.t3 Gene=g3900 Length=337
MDARTEEEKQKISWTHALRKIVINCYKYHGREDLLPAFSEEDEKANAIATANANYQTVLQ
TNPDGTFSLIQVDPSTLSNNPSIITLPDGTTAQVQGVATLHTQSDGTTVHTVQALDGQTE
NMQVDLSEALAQDGQLIITNEDGNGPYPVFVSLPVTAQMYHSLVQQQIPNSDNTVCVTPM
QVQNFITSNSLCCASITNQNSTTYLMAANNNGSKNVVNLPFQTTSATNCHIKSVLANPKA
SKIRTAVIKKPLIKKQRILNVAVAKVKPKIDNIKVISGTISHTDNNNTKKVKDKNEKLSQ
EDIKILPKKSKNIQTKVSLKHIELKLKKESSLEKKQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g3900.t3 | PANTHER | PTHR20338 | NUCLEAR RESPIRATORY FACTOR 1 | 1 | 201 | 0.0e+00 |
| 4 | g3900.t3 | PANTHER | PTHR20338:SF8 | NUCLEAR RESPIRATORY FACTOR 1 | 1 | 201 | 0.0e+00 |
| 1 | g3900.t3 | Pfam | PF10491 | NLS-binding and DNA-binding and dimerisation domains of Nrf1 | 2 | 38 | 0.0e+00 |
| 2 | g3900.t3 | Pfam | PF10492 | Nrf1 activator activation site binding domain | 151 | 225 | 2.8e-05 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006357 | regulation of transcription by RNA polymerase II | BP |
| GO:0003700 | DNA-binding transcription factor 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.
