General information for g9933.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ferredoxin-dependent glutamate synthase 1.
Parent gene
- The parent gene g9933 is located on chr_1: 6076806..6087141 (+ 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_1 | g9933 | g9933.t3 | isoform | g9933.t3 | 6071941 | 6081097 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon1 | 6071941 | 6072152 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon2 | 6076501 | 6077006 |
| chr_1 | g9933 | g9933.t3 | cds | g9933.t3.CDS1 | 6076806 | 6077006 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon3 | 6077422 | 6077549 |
| chr_1 | g9933 | g9933.t3 | cds | g9933.t3.CDS2 | 6077422 | 6077549 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon4 | 6079509 | 6079670 |
| chr_1 | g9933 | g9933.t3 | cds | g9933.t3.CDS3 | 6079509 | 6079670 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon5 | 6079734 | 6079824 |
| chr_1 | g9933 | g9933.t3 | cds | g9933.t3.CDS4 | 6079734 | 6079824 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon6 | 6079892 | 6080222 |
| chr_1 | g9933 | g9933.t3 | cds | g9933.t3.CDS5 | 6079892 | 6080222 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon7 | 6080278 | 6080384 |
| chr_1 | g9933 | g9933.t3 | cds | g9933.t3.CDS6 | 6080278 | 6080384 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon8 | 6080443 | 6080641 |
| chr_1 | g9933 | g9933.t3 | cds | g9933.t3.CDS7 | 6080443 | 6080641 |
| chr_1 | g9933 | g9933.t3 | exon | g9933.t3.exon9 | 6080701 | 6081097 |
| chr_1 | g9933 | g9933.t3 | cds | g9933.t3.CDS8 | 6080701 | 6080777 |
| chr_1 | g9933 | g9933.t3 | TSS | g9933.t3 | NA | NA |
| chr_1 | g9933 | g9933.t3 | TTS | g9933.t3 | NA | NA |
Sequences
>g9933.t3 Gene=g9933 Length=2133
TCTCTCAGTCGTATTGTTCGCTCGCTCGAGACAAGTCGTAAAAAGGCAAAGCTCCCAAGA
AAATTCATTTATCGCGTGAAAATTCTTAAAGTGAAGTGAGAAAGTACATGAGAAAAAAGT
CATTTTTGTAACTTTAATAAATTTGTGCACATTTCTGCGAAAAGTTATCAGATTTCATTC
TTAAAACCACAAACATTGTAAATTTATATTGTATTGGTCTTCCTCAAAATTCTACAATTT
TTATTTTCAATAAATATCGACCATAAAAATATTTTATTTGTCGCTTTCGCTCAAATCTAA
TAAGATTATCACATAATTCTTTACAAAGAACAATACGATACACTTGCTTTTAATTTCAAT
TCTTATTGACTCTTATTACAAATAGTATCCAGTAAGAAAATTAAATATTAAAAACACAAT
ATAAATTATAATTTAGGTTTTAAATTACAATATAAATTTCGCAAAGCGAAGAAAAATAAA
TAAATTTATAAGAAAAGCAACGAGCATTGAATAAAAGATGTCTCCACCCTGCACGAATGA
TTGCAATGCGACAAGGCCTGATGTTATGAGTAGCGATAATGAAATAAGAGAGAATGTTGA
GGAAAAATTAATGGATTGGGAAGCTCCAAAAAAACAAGGACTTTATGATCCACAGAATGA
GCATGACGCTTGTGGTGTTGGATTCATCGTTGCTATCGATGGACGTCGTCATCATAAGAT
ATTACGTGATGCTCAAACATTGGCTGAACGTATGTATCACAGAGGCGCTGTTGCATGCGA
TAATGATACTGGTGATGGATCTGGCGTCATGACAGCTATTCCTCATAAACTTTATGCAAA
GGAATTAGCATCGCAGGGAATTTCGTTGCCCGAGTTTGGTAAATATGCAACTGGTATCAT
TTACTTGGACAAGGATACTCATCTGGAAGCTGAAAAGGACTTTAATACTTTGGCTGCAAG
TCTTGGTATTAATGTAATTGCTTGGCGAACAGTTCCAACTGATTCGAGTGCAATTGGTGC
AGTTGCTCGTAAAAGTGAACCTTTGTCACGCCAAGTTTTTGTCACTGCTGACTTGGACGA
AGAGGCATTAAAGAAAAAGGTGTTCGTGCTTCGTAAACGTGCAACACATGAGCTGGTTAA
ACCAGGCCGTCGTTTCTACATTAAATCGTTATCAACGCTAACAATCGTCTATAAAGGTCT
CTTCAATTCTGATCAATTGTGGTTATATTATACAGATCTTCTCAATCCTGATTTTGACAC
CTATTTGGCTCTTGTTCATACGCGCTTCAGCACAAATACCTTTCCAGCATGGGAGCGTGC
ACATCCAATGCGTGTTTTAGCACATAACGGTGAAATTAACACATTGCGTGGAAATGTCAA
TTTAATGAAGGCTCGTGAAGGTGTCATGAAGAGCGATGAATTTGGAGATGAATTGAAAAA
ACTCTTTCCTGTCGTTGAGCCGAATTTATCCGATTCTGGCTCAGCGGATTGTGTGCTTGA
ATTTTTAACTATGGCTGGTAAAAGATCTTTGCCTGAGGCTGTAATGACAATGGTCCCAGA
AGCATGGCATAATGATAAGACAATGTCACAAGAAAAGCGTGACTTTTATCGTTGGGCTGC
TTGCGTTATGGAGCCTTGGGATGGCCCAGCATTGATTTCATTCACAGACGGTCGATATAT
TGGCGCTGTTTTAGATCGTAATGGATTACGTCCATCTCGTTTTTATGTCACAAGAGATAA
TATTCTCGTAATGGCATCTGAGGTTGGAGTTTATGATGTTGAACCTAAAGATGTTTTATT
GAAGGTAGAATAAAAAAATTCATTTTCTAAAGTTTAAGATCAACAAACTTTTATAGATCA
AAGTATCAGGCGAATGGTTAGAGAGTGATAGTGAAAGCTCGATATTTGGATCGTGATTTT
ATTAAGTATATCTTTAATCCTTAAGCCATTTTGAATTTATTCAATTACGCAATTATATAA
TTCGAAGCTATAGCTCGCTCTCAAATATAAAGTTCTTTTTCCCTTGTTTATACACGCTTT
TCTCTAGCATGTATATTTATGCTTAATAAAACATAACATTTTGAGCTTCTCTTAATGTCT
TGTAATCCCATTATTTCTTTTTCTTGTTACAGA
>g9933.t3 Gene=g9933 Length=431
MSPPCTNDCNATRPDVMSSDNEIRENVEEKLMDWEAPKKQGLYDPQNEHDACGVGFIVAI
DGRRHHKILRDAQTLAERMYHRGAVACDNDTGDGSGVMTAIPHKLYAKELASQGISLPEF
GKYATGIIYLDKDTHLEAEKDFNTLAASLGINVIAWRTVPTDSSAIGAVARKSEPLSRQV
FVTADLDEEALKKKVFVLRKRATHELVKPGRRFYIKSLSTLTIVYKGLFNSDQLWLYYTD
LLNPDFDTYLALVHTRFSTNTFPAWERAHPMRVLAHNGEINTLRGNVNLMKAREGVMKSD
EFGDELKKLFPVVEPNLSDSGSADCVLEFLTMAGKRSLPEAVMTMVPEAWHNDKTMSQEK
RDFYRWAACVMEPWDGPALISFTDGRYIGAVLDRNGLRPSRFYVTRDNILVMASEVGVYD
VEPKDVLLKVE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9933.t3 | CDD | cd00713 | GltS | 52 | 429 | 0.000 |
| 5 | g9933.t3 | Gene3D | G3DSA:3.60.20.10 | Glutamine Phosphoribosylpyrophosphate | 52 | 431 | 0.000 |
| 2 | g9933.t3 | PANTHER | PTHR11938 | FAD NADPH DEHYDROGENASE/OXIDOREDUCTASE | 28 | 429 | 0.000 |
| 3 | g9933.t3 | PANTHER | PTHR11938:SF133 | GLUTAMATE SYNTHASE [NADH] | 28 | 429 | 0.000 |
| 1 | g9933.t3 | Pfam | PF00310 | Glutamine amidotransferases class-II | 52 | 429 | 0.000 |
| 6 | g9933.t3 | ProSiteProfiles | PS51278 | Glutamine amidotransferase type 2 domain profile. | 52 | 431 | 20.298 |
| 4 | g9933.t3 | SUPERFAMILY | SSF56235 | N-terminal nucleophile aminohydrolases (Ntn hydrolases) | 52 | 428 | 0.000 |
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.
