General information for g1671.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glutamate decarboxylase 2.
Parent gene
- The parent gene g1671 is located on chr_3: 12376630..12378337 (+ 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 | g1671 | g1671.t2 | isoform | g1671.t2 | 12376630 | 12378337 |
| chr_3 | g1671 | g1671.t2 | exon | g1671.t2.exon1 | 12376630 | 12376786 |
| chr_3 | g1671 | g1671.t2 | cds | g1671.t2.CDS1 | 12376714 | 12376786 |
| chr_3 | g1671 | g1671.t2 | exon | g1671.t2.exon2 | 12376881 | 12376943 |
| chr_3 | g1671 | g1671.t2 | cds | g1671.t2.CDS2 | 12376881 | 12376943 |
| chr_3 | g1671 | g1671.t2 | exon | g1671.t2.exon3 | 12377002 | 12377149 |
| chr_3 | g1671 | g1671.t2 | cds | g1671.t2.CDS3 | 12377002 | 12377149 |
| chr_3 | g1671 | g1671.t2 | exon | g1671.t2.exon4 | 12377368 | 12378337 |
| chr_3 | g1671 | g1671.t2 | cds | g1671.t2.CDS4 | 12377368 | 12377962 |
| chr_3 | g1671 | g1671.t2 | TSS | g1671.t2 | NA | NA |
| chr_3 | g1671 | g1671.t2 | TTS | g1671.t2 | NA | NA |
Sequences
>g1671.t2 Gene=g1671 Length=1338
AACAAAGGCTTACATAATTTACCACGACTGGTAATTTTTACATCTATTGATGCTCACTAT
TCAGTAAAAAAATTGGCATCATTTATGGGCATTGGGAATGATAATGTCTACTTGATAAAT
ACAGACGAGATTGGAAAAATGGATATGAATCATTTAGAAAGTGAAATTTTGCGTGCAAAA
AATGAAGGAGCATTGCCGTTCATGGTTTCAGCCACGGCTGGCACCACTGTGTTAGGTGCA
TTCGATCCACTCGAGAAGATTGCTGATTTGTGTGAAAAATATAAAATATGGATGCATGTA
GATGCCGCCTGGGGAGGAGGTGCCTTAATGTCTAAAAAATATAAAAAATTGCTTAAAGGT
ATTGAGAGATCTGATTCAGTCACATGGAATCCACATAAAATGTTGGCATGTCCACAACAA
TGCAGTACATTCCTTTGTCGACATGAGGGTATTTTATCAGAATGTCACTCATCAAATGCC
GCATACTTGTTTCAAAAAGACAAGTTCTATGATACCAAATTTGATACGGGAGATAAACAT
ATTCAATGCGGAAGACGTGCTGACGTTTATAAATTTTGGTACATGTGGCGTGCAAAGGGA
ACAAAAGGATTTGAAAAACACATCGATTCAATTTTCGAAAAGGCCGAATATTTTACTGAT
CTTGTGAAAAAACAAGAAGGATTCGAACTTGTTTCACCTCCTGAATGCACAAATGTTTGC
TTTTGGTATATACCAAAAAGATTGAGAAATCTTCCACGTGATGAACATTTTGTTCAAGAA
TTACACAAAATTGCACCAAAAGTTAAAGAAAGAATGATGAAAAATGGCAGCATGATGATC
ACATATCAACCACTAAGAACAAAACCAAATTTCTTCCGTCTTGTTTTACAAGATTCATCA
CTCACACATCAAGATATGATGCATTTTGTTAATACTATTGAAAAATATAGTGAGGAGCTT
TAAATTCGTTTATTAAGACATCTACTAAATTTTTTAGGCAATAAAACTTAAATTTAAACT
TGATAATAATTGCTTAATCAATTCACACAACTCGGAAAAGCAATACAATGGAATTCGTTT
ATTGCGAAAATATAAACTAGATGAGGAACACCATTGTTGTTCAATGGCAAGAAATAAAGA
GTGATAGAAATACATGAAAAGAATTGCCAAAATGAACTTGAAAAAAAAAATTAAAATAAA
TGAACCAAAAATATATATTTTATGGTTCAAACACGTATCATCAAATCAAAAACATTGTTT
ATATGTATGCATATTACTTATTATTATATTCAAAGAAAAATGCTGTAATAAAATTTTAAT
TTTATTTGGATGATTAAA
>g1671.t2 Gene=g1671 Length=292
MGIGNDNVYLINTDEIGKMDMNHLESEILRAKNEGALPFMVSATAGTTVLGAFDPLEKIA
DLCEKYKIWMHVDAAWGGGALMSKKYKKLLKGIERSDSVTWNPHKMLACPQQCSTFLCRH
EGILSECHSSNAAYLFQKDKFYDTKFDTGDKHIQCGRRADVYKFWYMWRAKGTKGFEKHI
DSIFEKAEYFTDLVKKQEGFELVSPPECTNVCFWYIPKRLRNLPRDEHFVQELHKIAPKV
KERMMKNGSMMITYQPLRTKPNFFRLVLQDSSLTHQDMMHFVNTIEKYSEEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1671.t2 | Gene3D | G3DSA:3.40.640.10 | - | 3 | 137 | 0 |
| 5 | g1671.t2 | Gene3D | G3DSA:3.90.1150.170 | - | 138 | 291 | 0 |
| 2 | g1671.t2 | PANTHER | PTHR45677:SF12 | BLACK, ISOFORM A | 1 | 291 | 0 |
| 3 | g1671.t2 | PANTHER | PTHR45677 | GLUTAMATE DECARBOXYLASE-RELATED | 1 | 291 | 0 |
| 1 | g1671.t2 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 9 | 215 | 0 |
| 4 | g1671.t2 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 2 | 291 | 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:0019752 | carboxylic acid metabolic process | BP |
| GO:0016831 | carboxy-lyase activity | MF |
| GO:0003824 | catalytic activity | MF |
| GO:0030170 | pyridoxal phosphate binding | 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.
