General information for g13945.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glutamate decarboxylase.
Parent gene
- The parent gene g13945 is located on chr_1: 33541513..33542498 (- 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 | g13945 | g13945.t12 | TTS | g13945.t12 | 33540211 | 33540211 |
| chr_1 | g13945 | g13945.t12 | isoform | g13945.t12 | 33540815 | 33542498 |
| chr_1 | g13945 | g13945.t12 | exon | g13945.t12.exon1 | 33540815 | 33540913 |
| chr_1 | g13945 | g13945.t12 | cds | g13945.t12.CDS1 | 33540815 | 33540913 |
| chr_1 | g13945 | g13945.t12 | exon | g13945.t12.exon2 | 33541252 | 33541622 |
| chr_1 | g13945 | g13945.t12 | cds | g13945.t12.CDS2 | 33541252 | 33541622 |
| chr_1 | g13945 | g13945.t12 | exon | g13945.t12.exon3 | 33542000 | 33542335 |
| chr_1 | g13945 | g13945.t12 | cds | g13945.t12.CDS3 | 33542000 | 33542335 |
| chr_1 | g13945 | g13945.t12 | exon | g13945.t12.exon4 | 33542387 | 33542498 |
| chr_1 | g13945 | g13945.t12 | cds | g13945.t12.CDS4 | 33542387 | 33542498 |
| chr_1 | g13945 | g13945.t12 | TSS | g13945.t12 | 33542545 | 33542545 |
Sequences
>g13945.t12 Gene=g13945 Length=918
ATGTCATCAGTTCATCCGGACGTTTACAAATTACAGGCAAAAATCGCCGATTTAACTTGT
TATGATCTGTTGCCCTTTAAAGAAGGAGCACATCGTGAAACACGGGAATTTTGCAATGAA
CACGTTTTAGAATATCATTCACCTGATAAGCTCAAAGAATTATTCAATATGGTTGTTCCT
CATGATGGAATGACCCTTCAACATTTGATCACCGATTGTGCTACTGTTTTGAAATATGGA
GTCAAAACTGGTCACCCGCACTTTATGAATCAACTCTCATGTGGCCTTGATATCATCTCT
ATGGCTGGAGAATGGCTAACAGCGACTGCAAACTGTAATATGTTTACATATGAAATTTCG
CCTGTTTTTATCATTATGGAACATCAAGTGCTTAAACGTATGAGAAGAATTATTGGGTGG
CATTCAGGAGATTCTATTATGTCACCAGGTGGCACGATCAGTAATCTGTATTCAGTAATT
GTCGCACGTTATAAAATGTTCCCAGATTACAAAGTTCAAGGTCAAAAAGCATTGCCAGGT
GAATTGGTTATTTTTACAACTGATCAAGGCCATTATTCAATGAAGATGGCAGCTATGATT
TGTGGTTTGGGAACATCTAATTGCATTTATGTGAAGAGTGATAAACGAGGCAAGATGATT
CCGAGTGAACTTGAGCGACACATTCTTGAAGAGAAGGCAAAGGGTAAATACCCAATTATG
GTTAATGGCACAGCTGGTACAACTGTTTTGGGTGCATTTGATCCAATCAATGACCTTGCT
GATATCTGTGAAAAGTATGGGCTATGGCTTCATATTGATGGCGCTTGGGGAGGTTCTATG
GTTCTCTCACACAAGCATCGTACAACTCGACTTCAAGGAATTGAACGTGCTAACTCAATT
ACATGGAATCCACATAAA
>g13945.t12 Gene=g13945 Length=306
MSSVHPDVYKLQAKIADLTCYDLLPFKEGAHRETREFCNEHVLEYHSPDKLKELFNMVVP
HDGMTLQHLITDCATVLKYGVKTGHPHFMNQLSCGLDIISMAGEWLTATANCNMFTYEIS
PVFIIMEHQVLKRMRRIIGWHSGDSIMSPGGTISNLYSVIVARYKMFPDYKVQGQKALPG
ELVIFTTDQGHYSMKMAAMICGLGTSNCIYVKSDKRGKMIPSELERHILEEKAKGKYPIM
VNGTAGTTVLGAFDPINDLADICEKYGLWLHIDGAWGGSMVLSHKHRTTRLQGIERANSI
TWNPHK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13945.t12 | Gene3D | G3DSA:3.90.1150.170 | - | 14 | 114 | 0 |
| 6 | g13945.t12 | Gene3D | G3DSA:3.40.640.10 | - | 115 | 306 | 0 |
| 2 | g13945.t12 | PANTHER | PTHR45677:SF10 | GLUTAMATE DECARBOXYLASE | 39 | 306 | 0 |
| 3 | g13945.t12 | PANTHER | PTHR45677 | GLUTAMATE DECARBOXYLASE-RELATED | 39 | 306 | 0 |
| 1 | g13945.t12 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 48 | 306 | 0 |
| 4 | g13945.t12 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 35 | 306 | 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.
