General information for g13945.t1
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.t1 | TTS | g13945.t1 | 33540211 | 33540211 |
| chr_1 | g13945 | g13945.t1 | isoform | g13945.t1 | 33540248 | 33542498 |
| chr_1 | g13945 | g13945.t1 | exon | g13945.t1.exon1 | 33540248 | 33540913 |
| chr_1 | g13945 | g13945.t1 | cds | g13945.t1.CDS1 | 33540248 | 33540913 |
| chr_1 | g13945 | g13945.t1 | exon | g13945.t1.exon2 | 33541252 | 33541622 |
| chr_1 | g13945 | g13945.t1 | cds | g13945.t1.CDS2 | 33541252 | 33541622 |
| chr_1 | g13945 | g13945.t1 | exon | g13945.t1.exon3 | 33542000 | 33542498 |
| chr_1 | g13945 | g13945.t1 | cds | g13945.t1.CDS3 | 33542000 | 33542498 |
| chr_1 | g13945 | g13945.t1 | TSS | g13945.t1 | 33542545 | 33542545 |
Sequences
>g13945.t1 Gene=g13945 Length=1536
ATGTCATCAGTTCATCCGGACGTTTACAAATTACAGGCAAAAATCGCCGATTTAACTTGT
TATGATCTGTTGCCCTTTAAAGAAGGAGCACATCGTGAAACACGGGAATTTTTGCAAAAA
ATTGTTGACATTCTGCTCGACTACATTGAACTCTGTTACGATCGCAATGAACACGTTTTA
GAATATCATTCACCTGATAAGCTCAAAGAATTATTCAATATGGTTGTTCCTCATGATGGA
ATGACCCTTCAACATTTGATCACCGATTGTGCTACTGTTTTGAAATATGGAGTCAAAACT
GGTCACCCGCACTTTATGAATCAACTCTCATGTGGCCTTGATATCATCTCTATGGCTGGA
GAATGGCTAACAGCGACTGCAAACTGTAATATGTTTACATATGAAATTTCGCCTGTTTTT
ATCATTATGGAACATCAAGTGCTTAAACGTATGAGAAGAATTATTGGGTGGCATTCAGGA
GATTCTATTATGTCACCAGGTGGCACGATCAGTAATCTGTATTCAGTAATTGTCGCACGT
TATAAAATGTTCCCAGATTACAAAGTTCAAGGTCAAAAAGCATTGCCAGGTGAATTGGTT
ATTTTTACAACTGATCAAGGCCATTATTCAATGAAGATGGCAGCTATGATTTGTGGTTTG
GGAACATCTAATTGCATTTATGTGAAGAGTGATAAACGAGGCAAGATGATTCCGAGTGAA
CTTGAGCGACACATTCTTGAAGAGAAGGCAAAGGGTAAATACCCAATTATGGTTAATGGC
ACAGCTGGTACAACTGTTTTGGGTGCATTTGATCCAATCAATGACCTTGCTGATATCTGT
GAAAAGTATGGGCTATGGCTTCATATTGATGGCGCTTGGGGAGGTTCTATGGTTCTCTCA
CACAAGCATCGTACAACTCGACTTCAAGGAATTGAACGTGCTAACTCAATTACATGGAAT
CCACATAAACTTATGGGTGTTATCCTTCAATGTTCGACCTTTCATGTACGTGAAAGTGGT
TTGCTTGAACATTGCAACCGCATGACAGCCGAATATTTGTTTATGACCGACAAATTTTAT
GACACTCACTATGACACAGGTGATCGTGTCATTCAATGCGGTCGTCATAATGATATTTTT
AAATTGTGGTTCTCATGGCGTGCTCGTGGTGAAGCAGGCTTTGAAGCTCGTGTAGATCGA
TTTATGGAGCTTGCTCAATACCAAGTGAAGAGAATTAAAGAAATGCCAGACAAATTTTAT
CTGCTCATGGAGCCAGAATATGTCAATGTTTGCTTTTGGTATATTCCACAACGCTTTAGA
CATATGCCGCACAGTCCAGAAAAAGAAGAAGAGCTTGCTCGTCTCTGTCCAATTATCAAA
GAACGCATGATGAAAGCTGGCACACTCATGGTTGGCTATCAAAGAGATGGTAAAGTGCCA
AATTTCTTCCGTTCCATCATTTCTCAAGATGCCATTACTGAAAAGGACATTGACTTCATG
TTGCATGAAATTGATAGACTTGGTTACGATTTGTGA
>g13945.t1 Gene=g13945 Length=511
MSSVHPDVYKLQAKIADLTCYDLLPFKEGAHRETREFLQKIVDILLDYIELCYDRNEHVL
EYHSPDKLKELFNMVVPHDGMTLQHLITDCATVLKYGVKTGHPHFMNQLSCGLDIISMAG
EWLTATANCNMFTYEISPVFIIMEHQVLKRMRRIIGWHSGDSIMSPGGTISNLYSVIVAR
YKMFPDYKVQGQKALPGELVIFTTDQGHYSMKMAAMICGLGTSNCIYVKSDKRGKMIPSE
LERHILEEKAKGKYPIMVNGTAGTTVLGAFDPINDLADICEKYGLWLHIDGAWGGSMVLS
HKHRTTRLQGIERANSITWNPHKLMGVILQCSTFHVRESGLLEHCNRMTAEYLFMTDKFY
DTHYDTGDRVIQCGRHNDIFKLWFSWRARGEAGFEARVDRFMELAQYQVKRIKEMPDKFY
LLMEPEYVNVCFWYIPQRFRHMPHSPEKEEELARLCPIIKERMMKAGTLMVGYQRDGKVP
NFFRSIISQDAITEKDIDFMLHEIDRLGYDL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13945.t1 | CDD | cd06450 | DOPA_deC_like | 105 | 507 | 2.83426E-116 |
| 6 | g13945.t1 | Gene3D | G3DSA:3.90.1150.170 | - | 45 | 508 | 4.1E-191 |
| 7 | g13945.t1 | Gene3D | G3DSA:3.40.640.10 | - | 130 | 378 | 4.1E-191 |
| 2 | g13945.t1 | PANTHER | PTHR45677:SF10 | GLUTAMATE DECARBOXYLASE | 13 | 511 | 6.1E-234 |
| 3 | g13945.t1 | PANTHER | PTHR45677 | GLUTAMATE DECARBOXYLASE-RELATED | 13 | 511 | 6.1E-234 |
| 1 | g13945.t1 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 65 | 434 | 5.6E-125 |
| 5 | g13945.t1 | ProSitePatterns | PS00392 | DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. | 316 | 337 | - |
| 4 | g13945.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 32 | 508 | 2.51E-118 |
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 transcript has been annotated with K01580 (glutamate decarboxylase)
Pathway
- This transcript belongs to the following pathways
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.
