Gene loci information

Transcript annotation

  • This transcript has been annotated as Glutamate decarboxylase.

Parent gene

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_2 g6738 g6738.t1 isoform g6738.t1 18414248 18423662
chr_2 g6738 g6738.t1 exon g6738.t1.exon1 18414248 18414421
chr_2 g6738 g6738.t1 cds g6738.t1.CDS1 18414248 18414421
chr_2 g6738 g6738.t1 exon g6738.t1.exon2 18414492 18414836
chr_2 g6738 g6738.t1 cds g6738.t1.CDS2 18414492 18414836
chr_2 g6738 g6738.t1 exon g6738.t1.exon3 18415046 18415124
chr_2 g6738 g6738.t1 cds g6738.t1.CDS3 18415046 18415124
chr_2 g6738 g6738.t1 exon g6738.t1.exon4 18416785 18416852
chr_2 g6738 g6738.t1 cds g6738.t1.CDS4 18416785 18416852
chr_2 g6738 g6738.t1 exon g6738.t1.exon5 18416908 18417414
chr_2 g6738 g6738.t1 cds g6738.t1.CDS5 18416908 18417414
chr_2 g6738 g6738.t1 exon g6738.t1.exon6 18417472 18417533
chr_2 g6738 g6738.t1 cds g6738.t1.CDS6 18417472 18417533
chr_2 g6738 g6738.t1 exon g6738.t1.exon7 18419016 18419252
chr_2 g6738 g6738.t1 cds g6738.t1.CDS7 18419016 18419252
chr_2 g6738 g6738.t1 exon g6738.t1.exon8 18421126 18421195
chr_2 g6738 g6738.t1 cds g6738.t1.CDS8 18421126 18421195
chr_2 g6738 g6738.t1 exon g6738.t1.exon9 18423591 18423662
chr_2 g6738 g6738.t1 cds g6738.t1.CDS9 18423591 18423662
chr_2 g6738 g6738.t1 TSS g6738.t1 NA NA
chr_2 g6738 g6738.t1 TTS g6738.t1 NA NA

Sequences

>g6738.t1 Gene=g6738 Length=1614
ATGGATAGTTTTCTAAAGCTAAAGTCAGAATTTGATAATCTTGTGTCAAAAATAAAAATT
CCTGGAGCAGAAACAAGAATGACGTCAATTGATCCCAGTAATTATAAATTGTCTGATAAG
ATTGCAAATCTTACAGAAAAAGATTTGTTGCCTCATATCGACACGGCACAGCCAGAAACA
CGCGAATTCCTTCAATGTGTCATCAACATTCTTCTGGACTATGTCAATGCATGCAACAAT
AGAAACGAAAAGATCTTAGAGTTTCATCATCCTGAAGATATGAAAAAGTTGTTGGATTTG
GACATCAATGACAATCCAGCACCATTGCAGCAATTGATTGTTGATTGTGCCACAACATTG
AAGTATCAAGTGAAAACTGGCCACCCTCACTTCTTTAATCAGCTGTCTTGTGGATTGGAC
ATCATCTCAATGGCTGGCGAGTGGTTAACAGCAACGGCAAATACAAACATGTTCACTTAT
GAAATTGCTCCAGTTTTTATTTTGATGGAAAATGTTGTGCTCTCGAAAATGCGCGATATT
ATTGGCTATAGTGGTGGAGATTCAATTTTGGCTCCTGGTGGTTCTATTTCAAACTTGTAC
GCCTTTCTTGCTGCACGTCATAAGATGTTCCCAGGCTACAAAGAACATGGACCAAGAGGT
CTTCCTGGTGATTTATGCATGTTTACATCTGATCAATCGCACTATTCTGTCAAATCCTGT
GCCTCTGTATGTGGTTTAGGAACTGAAAATTGTGTTATGGTTCCGTCCGATGAACATGGA
AAGATGATTGCAAGTGAACTTGAGCGATTGATTTTAGAACGAAAAGCACGTGGTCAAATT
CCATTCTTTGTTAGCGCGACTGCTGGCACAACTGTTTTGGGTGCTTTTGATCCATTAAAT
GAAATTGCTGATATTTGTGAAAAATACAATTGCTGGTTCCATGTCGATGCTGCATGGGGA
GGCGGATTGCTTCTTTCAAAGAAATATCGTCATCCACGATTATCGGGTATAGAAAGAAGT
CACAGTGTTACTTGGAATCCACATAAATTAATGGGTGCACTTTTACAATGTTCTAGCATC
CATTTTAGAGAAGATGGTTTGTTGCTTAGCTGTAACCAAATGTCAGCCGAATATCTTTTC
ATGACTGATAAACTTTACGATATTCAATATGATACTGGCGATAAAGTTATTCAATGTGGC
CGTCATAATGATATTTTCAAGTTGTGGCTTCAATGGCGTGCTAAGGGTGATGTTGGTTTT
GAAGCTCATATGGATCGATTGATGGAGTTGACACAGTATGAAGTAAAACGAATTAAAGAG
CAGTCAGATAAGTTTCATTTAATTTTGGAGCCTGAATTGGTAAATGTTTCATTCTGGTAC
ATTCCAAAACGACTTCGTGGTATTCCACATTCATCAGATAAAGAAAAAGAACTCGGCAAG
ATTTGCCCAATTATTAAAGCACGAATGATGCAAGCTGGAACTTTAATGGTTGGTTATCAA
CCTGATGATCGTCGTCCTAACTTTTTCCGATCAATCATCTCTTCAGCCGCTGTAACCGAA
AAAGATGTTGATTTTATGTTGGAAGAAATTGACCGCTTAGGTCAAGACTTGTAA

>g6738.t1 Gene=g6738 Length=537
MDSFLKLKSEFDNLVSKIKIPGAETRMTSIDPSNYKLSDKIANLTEKDLLPHIDTAQPET
REFLQCVINILLDYVNACNNRNEKILEFHHPEDMKKLLDLDINDNPAPLQQLIVDCATTL
KYQVKTGHPHFFNQLSCGLDIISMAGEWLTATANTNMFTYEIAPVFILMENVVLSKMRDI
IGYSGGDSILAPGGSISNLYAFLAARHKMFPGYKEHGPRGLPGDLCMFTSDQSHYSVKSC
ASVCGLGTENCVMVPSDEHGKMIASELERLILERKARGQIPFFVSATAGTTVLGAFDPLN
EIADICEKYNCWFHVDAAWGGGLLLSKKYRHPRLSGIERSHSVTWNPHKLMGALLQCSSI
HFREDGLLLSCNQMSAEYLFMTDKLYDIQYDTGDKVIQCGRHNDIFKLWLQWRAKGDVGF
EAHMDRLMELTQYEVKRIKEQSDKFHLILEPELVNVSFWYIPKRLRGIPHSSDKEKELGK
ICPIIKARMMQAGTLMVGYQPDDRRPNFFRSIISSAAVTEKDVDFMLEEIDRLGQDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6738.t1 CDD cd06450 DOPA_deC_like 131 533 1.16587E-120
6 g6738.t1 Gene3D G3DSA:3.90.1150.170 - 71 534 3.6E-194
7 g6738.t1 Gene3D G3DSA:3.40.640.10 - 156 404 3.6E-194
2 g6738.t1 PANTHER PTHR45677:SF10 GLUTAMATE DECARBOXYLASE 39 537 6.7E-258
3 g6738.t1 PANTHER PTHR45677 GLUTAMATE DECARBOXYLASE-RELATED 39 537 6.7E-258
1 g6738.t1 Pfam PF00282 Pyridoxal-dependent decarboxylase conserved domain 91 460 1.8E-138
5 g6738.t1 ProSitePatterns PS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. 342 363 -
4 g6738.t1 SUPERFAMILY SSF53383 PLP-dependent transferases 59 536 2.47E-121

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

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.

Raw TPM values