General information for g3900.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g3900.t1 | 28714001 | 28714001 |
| chr_3 | g3900 | g3900.t1 | isoform | g3900.t1 | 28714266 | 28718907 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon1 | 28714266 | 28714412 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS1 | 28714266 | 28714412 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon2 | 28714475 | 28714528 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS2 | 28714475 | 28714528 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon3 | 28715644 | 28715753 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS3 | 28715644 | 28715753 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon4 | 28715811 | 28715946 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS4 | 28715811 | 28715946 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon5 | 28716009 | 28716143 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS5 | 28716009 | 28716143 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon6 | 28717515 | 28717748 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS6 | 28717515 | 28717748 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon7 | 28717933 | 28718174 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS7 | 28717933 | 28718174 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon8 | 28718240 | 28718552 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS8 | 28718240 | 28718552 |
| chr_3 | g3900 | g3900.t1 | exon | g3900.t1.exon9 | 28718614 | 28718907 |
| chr_3 | g3900 | g3900.t1 | cds | g3900.t1.CDS9 | 28718614 | 28718907 |
| chr_3 | g3900 | g3900.t1 | TSS | g3900.t1 | NA | NA |
Sequences
>g3900.t1 Gene=g3900 Length=1665
ATGAATACCATAGCAACGACAGAGACTATAGAGATGGTTGATGAAGGAGGACTTACTGAT
GATTCAGAGTCTGATTTTGATAGTCGACCAAGCAGCCCAGACGAGGGAGATGGTAATTTA
CTAACTGAAGCTATGGAAAATGAAGTCACAGCACAACTTGTCAATGCTGGTGTCGTTGGA
ATAGCTGCTGCAGCTGCCATTACATCTTCAAAGAAAAGAAAACGTCCTCACTCGTTTGAA
ACAAATCCTTCCATCAGAAAACGACAACAAAATCGACTGCTAAGGAAATTGAGGCAAACA
ATATTTGAGTATGCAACACGAGTTGGTCAGCAAGCAGTCGTATTAGTTGCAACACCTGGT
AAACCGAACAATATTTACAAAGTTTTTGGCGCGAAACCTCTCGAAGATGTTATTAAAAAT
TTGCGCACGATGGTAATGGACGAACTCGAAACGGCATTAGCTCAACAAGCACCACCAAAA
GTACAGGAAGATCCATCACTGTTCGAATTGCCCCCTCTGATTATTGATGGGATTCCTACA
CCAGTCGAGAAGATGACACAAGCTCAATTGAGAGCATTTATTCCACTTATGCTTAAATAT
TCAACAGGACGAGGTAAACCAGGTTGGGGCCGTGATTCCACGCGGCCAGAATGGTGGCCT
AAAGAACTTCCATGGGCAAATGTGAGAATGGACGCACGAACAGAAGAAGAAAAACAAAAA
ATTAGCTGGACACATGCATTGCGAAAAATTGTTATAAACTGTTACAAATATCATGGACGA
GAAGACTTATTACCAGCATTCTCTGAAGAAGATGAAAAAGCAAATGCAATCGCAACTGCC
AATGCAAATGTTGGAGTTGTTAAAATTCAAAATCCAAATACATCAACGACTGTCAGTACG
AATCAATCAACTACAGTAGTCACTACGACAGCAGCTAGTAATACAAATTCTACAACCAAT
ACCATTACGCTACCAAAAATTGAAGTTCCCGCATCAACCACCATACAGATTCAATCATCT
AATCAGGCTATAGCGAACTCAGCTCAAGTTTGCATAGACACAATGCCACTCACTGAAGTT
GATTATCAAACAGTCTTACAAACTAATCCAGATGGAACATTCTCATTAATTCAAGTTGAT
CCAAGTACATTATCAAATAATCCATCGATAATCACTTTACCTGATGGTACAACAGCTCAA
GTTCAAGGTGTTGCTACTTTGCATACACAAAGTGATGGCACAACTGTCCATACAGTCCAA
GCTCTTGATGGTCAAACAGAAAATATGCAAGTAGATCTCTCAGAAGCTCTTGCTCAAGAT
GGTCAACTAATAATCACAAATGAAGATGGAAATGGCCCATATCCAGTGTTTGTTTCTCTA
CCAGTTACCGCACAAATGTATCATTCACTCGTGCAGCAACAAATTCCAAATTCTGACAAT
ACAGTTTGTGTGACTCCTATGCAGATGGAAAGCAGTGAACCAATGGAAACAATTACGCTC
AATTCTTCAAATCTTAAGCTCTTCGACTCTTCAGCATCGAATATGCCTCAAGTCATGATT
CAAGGCGCTAATGGCGAACTAAAAATGTTAAGTCTTGCTGATCTCAAATCATTGGGTGTG
AATTTAATTGAAGATGTCAAGTCGGAAGACCAAATAATGGGCTGA
>g3900.t1 Gene=g3900 Length=554
MNTIATTETIEMVDEGGLTDDSESDFDSRPSSPDEGDGNLLTEAMENEVTAQLVNAGVVG
IAAAAAITSSKKRKRPHSFETNPSIRKRQQNRLLRKLRQTIFEYATRVGQQAVVLVATPG
KPNNIYKVFGAKPLEDVIKNLRTMVMDELETALAQQAPPKVQEDPSLFELPPLIIDGIPT
PVEKMTQAQLRAFIPLMLKYSTGRGKPGWGRDSTRPEWWPKELPWANVRMDARTEEEKQK
ISWTHALRKIVINCYKYHGREDLLPAFSEEDEKANAIATANANVGVVKIQNPNTSTTVST
NQSTTVVTTTAASNTNSTTNTITLPKIEVPASTTIQIQSSNQAIANSAQVCIDTMPLTEV
DYQTVLQTNPDGTFSLIQVDPSTLSNNPSIITLPDGTTAQVQGVATLHTQSDGTTVHTVQ
ALDGQTENMQVDLSEALAQDGQLIITNEDGNGPYPVFVSLPVTAQMYHSLVQQQIPNSDN
TVCVTPMQMESSEPMETITLNSSNLKLFDSSASNMPQVMIQGANGELKMLSLADLKSLGV
NLIEDVKSEDQIMG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3900.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 14 | 35 | - |
| 5 | g3900.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 70 | 89 | - |
| 3 | g3900.t1 | PANTHER | PTHR20338 | NUCLEAR RESPIRATORY FACTOR 1 | 22 | 537 | 2.4E-163 |
| 4 | g3900.t1 | PANTHER | PTHR20338:SF8 | NUCLEAR RESPIRATORY FACTOR 1 | 22 | 537 | 2.4E-163 |
| 1 | g3900.t1 | Pfam | PF10491 | NLS-binding and DNA-binding and dimerisation domains of Nrf1 | 57 | 267 | 9.3E-113 |
| 2 | g3900.t1 | Pfam | PF10492 | Nrf1 activator activation site binding domain | 458 | 525 | 2.8E-7 |
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 transcript has been annotated with K11831 (nuclear respiratory factor 1)
Pathway
- This transcript belongs to the following pathways
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.
