General information for g13945.t4
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.t4 | isoform | g13945.t4 | 33540130 | 33540910 |
| chr_1 | g13945 | g13945.t4 | exon | g13945.t4.exon1 | 33540130 | 33540157 |
| chr_1 | g13945 | g13945.t4 | cds | g13945.t4.CDS1 | 33540130 | 33540157 |
| chr_1 | g13945 | g13945.t4 | exon | g13945.t4.exon2 | 33540252 | 33540910 |
| chr_1 | g13945 | g13945.t4 | cds | g13945.t4.CDS2 | 33540252 | 33540895 |
| chr_1 | g13945 | g13945.t4 | TSS | g13945.t4 | NA | NA |
| chr_1 | g13945 | g13945.t4 | TTS | g13945.t4 | NA | NA |
Sequences
>g13945.t4 Gene=g13945 Length=687
GCTTGGGGAGGTTCTATGGTTCTCTCACACAAGCATCGTACAACTCGACTTCAAGGAATT
GAACGTGCTAACTCAATTACATGGAATCCACATAAACTTATGGGTGTTATCCTTCAATGT
TCGACCTTTCATGTACGTGAAAGTGGTTTGCTTGAACATTGCAACCGCATGACAGCCGAA
TATTTGTTTATGACCGACAAATTTTATGACACTCACTATGACACAGGTGATCGTGTCATT
CAATGCGGTCGTCATAATGATATTTTTAAATTGTGGTTCTCATGGCGTGCTCGTGGTGAA
GCAGGCTTTGAAGCTCGTGTAGATCGATTTATGGAGCTTGCTCAATACCAAGTGAAGAGA
ATTAAAGAAATGCCAGACAAATTTTATCTGCTCATGGAGCCAGAATATGTCAATGTTTGC
TTTTGGTATATTCCACAACGCTTTAGACATATGCCGCACAGTCCAGAAAAAGAAGAAGAG
CTTGCTCGTCTCTGTCCAATTATCAAAGAACGCATGATGAAAGCTGGCACACTCATGGTT
GGCTATCAAAGAGATGGTAAAGTGCCAAATTTCTTCCGTTCCATCATTTCTCAAGATGCC
ATTACTGAAAAGGACATTGACTTCATGTTGCATGAAATTGATAGACTTGGTTACGATTTA
ATGTTTTGTTTTTTTTTTTCTTTCTTT
>g13945.t4 Gene=g13945 Length=224
MVLSHKHRTTRLQGIERANSITWNPHKLMGVILQCSTFHVRESGLLEHCNRMTAEYLFMT
DKFYDTHYDTGDRVIQCGRHNDIFKLWFSWRARGEAGFEARVDRFMELAQYQVKRIKEMP
DKFYLLMEPEYVNVCFWYIPQRFRHMPHSPEKEEELARLCPIIKERMMKAGTLMVGYQRD
GKVPNFFRSIISQDAITEKDIDFMLHEIDRLGYDLMFCFFFSFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13945.t4 | Gene3D | G3DSA:3.90.1150.170 | - | 22 | 218 | 2.9E-59 |
| 2 | g13945.t4 | PANTHER | PTHR45677:SF10 | GLUTAMATE DECARBOXYLASE | 1 | 215 | 1.3E-98 |
| 3 | g13945.t4 | PANTHER | PTHR45677 | GLUTAMATE DECARBOXYLASE-RELATED | 1 | 215 | 1.3E-98 |
| 1 | g13945.t4 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 3 | 138 | 3.5E-44 |
| 5 | g13945.t4 | ProSitePatterns | PS00392 | DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. | 20 | 41 | - |
| 4 | g13945.t4 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 10 | 212 | 8.71E-41 |
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: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. There were no conditions that were differentially expressed