Gene loci information

Transcript annotation

  • This transcript has been annotated as 3-4-dihydroxyphenylacetaldehyde synthase.

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 g5266 g5266.t1 TTS g5266.t1 8314240 8314240
chr_2 g5266 g5266.t1 isoform g5266.t1 8314399 8316343
chr_2 g5266 g5266.t1 exon g5266.t1.exon1 8314399 8315159
chr_2 g5266 g5266.t1 cds g5266.t1.CDS1 8314399 8315159
chr_2 g5266 g5266.t1 exon g5266.t1.exon2 8315239 8315734
chr_2 g5266 g5266.t1 cds g5266.t1.CDS2 8315239 8315734
chr_2 g5266 g5266.t1 exon g5266.t1.exon3 8315811 8315830
chr_2 g5266 g5266.t1 cds g5266.t1.CDS3 8315811 8315830
chr_2 g5266 g5266.t1 exon g5266.t1.exon4 8315902 8316116
chr_2 g5266 g5266.t1 cds g5266.t1.CDS4 8315902 8316116
chr_2 g5266 g5266.t1 exon g5266.t1.exon5 8316264 8316343
chr_2 g5266 g5266.t1 cds g5266.t1.CDS5 8316264 8316343
chr_2 g5266 g5266.t1 TSS g5266.t1 8316485 8316485

Sequences

>g5266.t1 Gene=g5266 Length=1572
ATGGATATCAATGAATTTAAAGAATTTGGACATGCTGCAATTGATTTTATAGTGGAATAT
TTAGAAACAATTCGTGATCGACCAGTGCTTTCATCAGTTGAACCAGAATATTTACATGAT
CTACTTCCATCTGAAATGCCCGAACAACCTGAAAAATGGCAGGATATTATGGAAGATTTG
AAAAATCAAATTCTACCTGGTTTGACACATTGGCAATCACCACACTTTCATGCTTTTTAT
CCATCACAATCGTCTTTTCCTTCAATAGTAGGAGAATTGCTGACAGCAGGAATTGGTGTT
GTTGGATTTAGCTGGATATGCAGTCCCGCTGCCACTGAACTCGAAGTGATTGTGATGGAT
TGGCTTGGAAAGTTTTTAAATTTGCCGAGTCATTTTCTACCAAGTGGCCAAGGAAATGGA
GGTGGTATTATTCAAGGAAGTGCTAGCGAGTCGATTCTTGTAGCAGTCCTTGCTGCCCGT
GAAGAAAAAGTTCGTGAGATGAAAATTAAACGCCCAGAACTCACAGAGGGAGAAATTCGT
TCTAAATTAGTTGGTTATGGTTCAATTCATTCGAATAGTGCAATTGAAAAATCAGGATTA
CTAGCTGCAACTAAAATGCGACTTCTCGATGCTGATGAAACATCAATTATGCGTGGAGAA
ACCGTTGAGAAGGCAATTCAAGCTGATCTAGCTGAAGATTTGATTCCGTACATATGTGTC
ACAACGATTGGAACAACTGGCACTTGTGCGTTTGATAATATGGAAGAAATTGGACCAGTT
TGCAAGAAATATTCCGTTTGGATGCATATTGATGCTGCATATGCAGGCGCTGTATTCTGT
TTACCAGAGTATGCACATATAATGAAAGGAATTGAGTATGGCGATTCAATAAATTTCAAT
TTACACAAATGGATGCTCGTAAATTTTGACTGTGCAGCAATGTGGATTAAAGATGCAGGA
AAATTAACCCAGTCATTCAATGTAGAGCGTATTTATTTAGATCACAAATATCAAGGTGCA
AGTAAAGCACCAGATTATCGTCATTGGCAACTCGCACTTGGACGTCGATTCCGTTCATTG
AGAGTTTGGATTACATTTAGAACTTATGGACAGCAGAAAATTCGAGAATGGCTTCGTAAA
CACATTTCATTAGCAAGTTTATTCTTAGAATATCTTGCAACAGATGATCGTTTTGAAGCA
ACTGGGCAATCACTTGCACTTGCATTTTTCCGCTTGAAAGGAGACGATACATTGACAAGG
AAACTTTTAGATCGCATAAATGATCGAAAAAATATTTACATGATTCCAGCATTCTATCAA
AACAAAGTGATTATCAGATTTGTTATTTGTGGTCTCGATCCAGTTGAAAAAGATATTGAA
TATGCATGGAATGAAATAAAAACAGTCGCTGATGAGTTGTTAGCAGAAAATGAAGCTGCA
GAAAAGTTGCAAATTAAACTTTCAGAAAATGCAGAAAATGAAATAGAGACAGTAAAAGAT
AAAGTAAACTTTGTTACGGAAAATATCTCTCAAAGCTTCTCAATTTGTGAGCAAGAGAAA
ACCGTTCATTAA

>g5266.t1 Gene=g5266 Length=523
MDINEFKEFGHAAIDFIVEYLETIRDRPVLSSVEPEYLHDLLPSEMPEQPEKWQDIMEDL
KNQILPGLTHWQSPHFHAFYPSQSSFPSIVGELLTAGIGVVGFSWICSPAATELEVIVMD
WLGKFLNLPSHFLPSGQGNGGGIIQGSASESILVAVLAAREEKVREMKIKRPELTEGEIR
SKLVGYGSIHSNSAIEKSGLLAATKMRLLDADETSIMRGETVEKAIQADLAEDLIPYICV
TTIGTTGTCAFDNMEEIGPVCKKYSVWMHIDAAYAGAVFCLPEYAHIMKGIEYGDSINFN
LHKWMLVNFDCAAMWIKDAGKLTQSFNVERIYLDHKYQGASKAPDYRHWQLALGRRFRSL
RVWITFRTYGQQKIREWLRKHISLASLFLEYLATDDRFEATGQSLALAFFRLKGDDTLTR
KLLDRINDRKNIYMIPAFYQNKVIIRFVICGLDPVEKDIEYAWNEIKTVADELLAENEAA
EKLQIKLSENAENEIETVKDKVNFVTENISQSFSICEQEKTVH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g5266.t1 Coils Coil Coil 470 508 -
15 g5266.t1 Gene3D G3DSA:1.20.1340.10 dopa decarboxylase 1 81 4.6E-34
16 g5266.t1 Gene3D G3DSA:3.40.640.10 - 83 379 4.3E-101
14 g5266.t1 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 380 485 1.2E-25
2 g5266.t1 PANTHER PTHR11999 GROUP II PYRIDOXAL-5-PHOSPHATE DECARBOXYLASE 1 497 4.2E-231
3 g5266.t1 PANTHER PTHR11999:SF60 3,4-DIHYDROXYPHENYLACETALDEHYDE SYNTHASE 1 497 4.2E-231
5 g5266.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 6 25 3.2E-63
11 g5266.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 29 46 3.2E-63
4 g5266.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 47 66 3.2E-63
8 g5266.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 73 92 3.2E-63
9 g5266.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 94 112 3.2E-63
7 g5266.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 113 132 3.2E-63
10 g5266.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 140 160 3.2E-63
6 g5266.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 352 367 3.2E-63
1 g5266.t1 Pfam PF00282 Pyridoxal-dependent decarboxylase conserved domain 35 412 2.9E-123
13 g5266.t1 ProSitePatterns PS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. 296 317 -
12 g5266.t1 SUPERFAMILY SSF53383 PLP-dependent transferases 1 473 3.17E-129

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5266/g5266.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5266.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0019752 carboxylic acid metabolic process BP
GO:0016831 carboxy-lyase activity MF
GO:0006520 cellular amino acid metabolic process BP
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