General information for g13945.t11
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.t11 | TTS | g13945.t11 | 33540211 | 33540211 |
| chr_1 | g13945 | g13945.t11 | isoform | g13945.t11 | 33540248 | 33542498 |
| chr_1 | g13945 | g13945.t11 | exon | g13945.t11.exon1 | 33540248 | 33540402 |
| chr_1 | g13945 | g13945.t11 | cds | g13945.t11.CDS1 | 33540402 | 33540402 |
| chr_1 | g13945 | g13945.t11 | exon | g13945.t11.exon2 | 33540486 | 33540913 |
| chr_1 | g13945 | g13945.t11 | cds | g13945.t11.CDS2 | 33540486 | 33540913 |
| chr_1 | g13945 | g13945.t11 | exon | g13945.t11.exon3 | 33541252 | 33541622 |
| chr_1 | g13945 | g13945.t11 | cds | g13945.t11.CDS3 | 33541252 | 33541622 |
| chr_1 | g13945 | g13945.t11 | exon | g13945.t11.exon4 | 33542000 | 33542498 |
| chr_1 | g13945 | g13945.t11 | cds | g13945.t11.CDS4 | 33542000 | 33542498 |
| chr_1 | g13945 | g13945.t11 | TSS | g13945.t11 | 33542545 | 33542545 |
Sequences
>g13945.t11 Gene=g13945 Length=1453
ATGTCATCAGTTCATCCGGACGTTTACAAATTACAGGCAAAAATCGCCGATTTAACTTGT
TATGATCTGTTGCCCTTTAAAGAAGGAGCACATCGTGAAACACGGGAATTTTTGCAAAAA
ATTGTTGACATTCTGCTCGACTACATTGAACTCTGTTACGATCGCAATGAACACGTTTTA
GAATATCATTCACCTGATAAGCTCAAAGAATTATTCAATATGGTTGTTCCTCATGATGGA
ATGACCCTTCAACATTTGATCACCGATTGTGCTACTGTTTTGAAATATGGAGTCAAAACT
GGTCACCCGCACTTTATGAATCAACTCTCATGTGGCCTTGATATCATCTCTATGGCTGGA
GAATGGCTAACAGCGACTGCAAACTGTAATATGTTTACATATGAAATTTCGCCTGTTTTT
ATCATTATGGAACATCAAGTGCTTAAACGTATGAGAAGAATTATTGGGTGGCATTCAGGA
GATTCTATTATGTCACCAGGTGGCACGATCAGTAATCTGTATTCAGTAATTGTCGCACGT
TATAAAATGTTCCCAGATTACAAAGTTCAAGGTCAAAAAGCATTGCCAGGTGAATTGGTT
ATTTTTACAACTGATCAAGGCCATTATTCAATGAAGATGGCAGCTATGATTTGTGGTTTG
GGAACATCTAATTGCATTTATGTGAAGAGTGATAAACGAGGCAAGATGATTCCGAGTGAA
CTTGAGCGACACATTCTTGAAGAGAAGGCAAAGGGTAAATACCCAATTATGGTTAATGGC
ACAGCTGGTACAACTGTTTTGGGTGCATTTGATCCAATCAATGACCTTGCTGATATCTGT
GAAAAGTATGGGCTATGGCTTCATATTGATGGCGCTTGGGGAGGTTCTATGGTTCTCTCA
CACAAGCATCGTACAACTCGACTTCAAGGAATTGAACGTGCTAACTCAATTACATGGAAT
CCACATAAACTTATGGGTGTTATCCTTCAATGTTCGACCTTTCATGTACGTGAAAGTGGT
TTGCTTGAACATTGCAACCGCATGACAGCCGAATATTTGTTTATGACCGACAAATTTTAT
GACACTCACTATGACACAGGTGATCGTGTCATTCAATGCGGTCGTCATAATGATATTTTT
AAATTGTGGTTCTCATGGCGTGCTCGTGGTGAAGCAGGCTTTGAAGCTCGTGTAGATCGA
TTTATGGAGCTTGCTCAATACCAAGTGAAGAGAATTAAAGAAATGCCAGACAAATTTTAT
CTGCTCATGGAGCCAGAATATGTCAATGTTTGCTTTTGAACGCATGATGAAAGCTGGCAC
ACTCATGGTTGGCTATCAAAGAGATGGTAAAGTGCCAAATTTCTTCCGTTCCATCATTTC
TCAAGATGCCATTACTGAAAAGGACATTGACTTCATGTTGCATGAAATTGATAGACTTGG
TTACGATTTGTGA
>g13945.t11 Gene=g13945 Length=432
MSSVHPDVYKLQAKIADLTCYDLLPFKEGAHRETREFLQKIVDILLDYIELCYDRNEHVL
EYHSPDKLKELFNMVVPHDGMTLQHLITDCATVLKYGVKTGHPHFMNQLSCGLDIISMAG
EWLTATANCNMFTYEISPVFIIMEHQVLKRMRRIIGWHSGDSIMSPGGTISNLYSVIVAR
YKMFPDYKVQGQKALPGELVIFTTDQGHYSMKMAAMICGLGTSNCIYVKSDKRGKMIPSE
LERHILEEKAKGKYPIMVNGTAGTTVLGAFDPINDLADICEKYGLWLHIDGAWGGSMVLS
HKHRTTRLQGIERANSITWNPHKLMGVILQCSTFHVRESGLLEHCNRMTAEYLFMTDKFY
DTHYDTGDRVIQCGRHNDIFKLWFSWRARGEAGFEARVDRFMELAQYQVKRIKEMPDKFY
LLMEPEYVNVCF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13945.t11 | Gene3D | G3DSA:3.90.1150.170 | - | 44 | 432 | 1.1E-164 |
| 7 | g13945.t11 | Gene3D | G3DSA:3.40.640.10 | - | 132 | 380 | 1.1E-164 |
| 2 | g13945.t11 | PANTHER | PTHR45677:SF10 | GLUTAMATE DECARBOXYLASE | 13 | 432 | 3.9E-197 |
| 3 | g13945.t11 | PANTHER | PTHR45677 | GLUTAMATE DECARBOXYLASE-RELATED | 13 | 432 | 3.9E-197 |
| 1 | g13945.t11 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 65 | 432 | 1.4E-123 |
| 5 | g13945.t11 | ProSitePatterns | PS00392 | DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. | 316 | 337 | - |
| 4 | g13945.t11 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 32 | 432 | 3.98E-109 |
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. There were no conditions that were differentially expressed