General information for g16540.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative FAD synthase.
Parent gene
- The parent gene g16540 is located on chr_4: 9853355..9855170 (+ 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_4 | g16540 | g16540.t3 | isoform | g16540.t3 | 9852370 | 9853355 |
| chr_4 | g16540 | g16540.t3 | exon | g16540.t3.exon1 | 9852370 | 9852626 |
| chr_4 | g16540 | g16540.t3 | cds | g16540.t3.CDS1 | 9852555 | 9852626 |
| chr_4 | g16540 | g16540.t3 | exon | g16540.t3.exon2 | 9852685 | 9853038 |
| chr_4 | g16540 | g16540.t3 | cds | g16540.t3.CDS2 | 9852685 | 9853038 |
| chr_4 | g16540 | g16540.t3 | exon | g16540.t3.exon3 | 9853107 | 9853355 |
| chr_4 | g16540 | g16540.t3 | cds | g16540.t3.CDS3 | 9853107 | 9853355 |
| chr_4 | g16540 | g16540.t3 | TTS | g16540.t3 | 9854338 | 9854338 |
| chr_4 | g16540 | g16540.t3 | TSS | g16540.t3 | NA | NA |
Sequences
>g16540.t3 Gene=g16540 Length=860
AAAAAATATTCTTCAACCTAAAATCGCTTTTTACCTGTTTCTTTTTCAATTCTTCTCAAA
TTCTTCTTTTCATTTTTACTCTCATTAAGTCTATTTGATAACACATAAACATCACGTCTA
AAATATTTTTAATTTTTCACAATTTTTGAATGGAAATTTAGTCAAAAGTTCGTCCTTCAT
CGATCATGACAGCAACGAATGGTCATCAGCCACCATTAACAAGTGATTTTGATACAAAAC
TTAAAAATTCATTTGATATCATTGAAAAAGCATTCCAACAATATGACACGCGACAAATTT
TCTTATCATTTAACGGCGGCAAGGACTGCACGGTGCTACTAGATTTAATCAAAAATTTTC
TTAAAAATTCCATCAGTGACCTTAAAATTTTCTATTTTCGTCAAACGAATCCATTTCCTG
AAATTGATGACTTTGTGAGTGGCTGTGAGCGACATTATGGTGTTAAGATTATTACATTAG
AAGCCAATTGTTCGATGAAGCAAATTTTAGAAGCTATTGTTGAAAATGATGATGATTTGG
CTGCTTGTTTTATGGGTTGCAGAAAAAATGATCCAACATATAAAAAAAGGGAGAAAGTTG
ACCCATTTGAGCCAACAGATAAAGGATGGCCACAGTTAATGCGTATAAATCCTCTCTTAG
ACTGGACATGCAAAGATATTTGGCAATATTTACTTCAAAATAAAGTTCCATATTGCTCTC
TTTATAACATTGGTTACACATCAATTGGCAATATGAAAAATACAATTCAAAATCCACACT
TAATTAATGATGATGGTGTAACTTATAAACCTGCCTTTGAATTATTGGATGATGAATTTG
AAAGAGCTGGACGATTGTGA
>g16540.t3 Gene=g16540 Length=224
MTATNGHQPPLTSDFDTKLKNSFDIIEKAFQQYDTRQIFLSFNGGKDCTVLLDLIKNFLK
NSISDLKIFYFRQTNPFPEIDDFVSGCERHYGVKIITLEANCSMKQILEAIVENDDDLAA
CFMGCRKNDPTYKKREKVDPFEPTDKGWPQLMRINPLLDWTCKDIWQYLLQNKVPYCSLY
NIGYTSIGNMKNTIQNPHLINDDGVTYKPAFELLDDEFERAGRL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g16540.t3 | CDD | cd01713 | PAPS_reductase | 37 | 188 | 0 |
| 5 | g16540.t3 | Gene3D | G3DSA:3.40.50.620 | HUPs | 2 | 224 | 0 |
| 2 | g16540.t3 | PANTHER | PTHR23293:SF9 | FAD SYNTHASE | 8 | 223 | 0 |
| 3 | g16540.t3 | PANTHER | PTHR23293 | FAD SYNTHETASE-RELATED FMN ADENYLYLTRANSFERASE | 8 | 223 | 0 |
| 1 | g16540.t3 | Pfam | PF01507 | Phosphoadenosine phosphosulfate reductase family | 106 | 193 | 0 |
| 4 | g16540.t3 | SUPERFAMILY | SSF52402 | Adenine nucleotide alpha hydrolases-like | 15 | 183 | 0 |
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:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00953 (FAD synthetase)
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.
