Gene loci information

Transcript annotation

  • This transcript has been annotated as Aromatic-L-amino-acid 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 g5265 g5265.t1 TSS g5265.t1 8311072 8311072
chr_2 g5265 g5265.t1 isoform g5265.t1 8311524 8314233
chr_2 g5265 g5265.t1 exon g5265.t1.exon1 8311524 8311550
chr_2 g5265 g5265.t1 cds g5265.t1.CDS1 8311524 8311550
chr_2 g5265 g5265.t1 exon g5265.t1.exon2 8311720 8311805
chr_2 g5265 g5265.t1 cds g5265.t1.CDS2 8311720 8311805
chr_2 g5265 g5265.t1 exon g5265.t1.exon3 8312673 8312817
chr_2 g5265 g5265.t1 cds g5265.t1.CDS3 8312673 8312817
chr_2 g5265 g5265.t1 exon g5265.t1.exon4 8312897 8313236
chr_2 g5265 g5265.t1 cds g5265.t1.CDS4 8312897 8313236
chr_2 g5265 g5265.t1 exon g5265.t1.exon5 8313297 8313850
chr_2 g5265 g5265.t1 cds g5265.t1.CDS5 8313297 8313850
chr_2 g5265 g5265.t1 exon g5265.t1.exon6 8313916 8314233
chr_2 g5265 g5265.t1 cds g5265.t1.CDS6 8313916 8314233
chr_2 g5265 g5265.t1 TTS g5265.t1 8314346 8314346

Sequences

>g5265.t1 Gene=g5265 Length=1470
ATGGCTAACAAAAAATCATTGGAATCTATCGACATGGAAGCACCTGAGTTTAAAGACTTT
GCCAAGTCAATGGTTGACTATATCGCAAACTATCTGGAGAATATTCGTGATAGGCCAGTT
TTGCCATCAGTTCAACCAGGTTATTTAGAAAAATTAATTCCATCTGAAGCTCCCTCAAAA
CCAGAAAGTTGGACTGATGTTATGGCAGATATTGAAAGAGTTATCATGCCTGGTGTGACT
CATTGGCATTCGCCTAGATTTCATGCATATTTCCCAACCGCAAATTCTTACCCAGCTATT
GTTGCTGATATGTTAAGTGGTGCGATCGCTTGTATTGGTTTCACATGGATTGCTAGTCCG
GCATGTACTGAATTAGAAGTTGTCATGATGGATTGGCTAGGAAAAATGATTGGTTTGCCA
GCAGAATTTCTTGCATGTTCAGGTGGAAAAGGTGGCGGTGTTATACAAGGAACAGCTAGT
GAAGCTACACTTGTTGGTTTATTAGGTGCAAAAGCAAAAATGATGCAGCGAATGAAAGCG
GAACATCCAGATTGGGATGATAATACAATTGTCTCAAAATTGGTCGCTTATTGCTCAAAT
CAAGCACATTCATCAGTTGAAAGAGCTGGTCTATTGGGAGGCGTGCAAATGAGAAGTTTG
AAAGCTGATGATAATTTGCAATTGAGAGGCGAAACATTAGAAGAAGCGATTAAAAAAGAT
TTAGCTGATGGTTTAATTCCATTTTATGTGGTTGCAACATTGGGTACAACGAACTCTTGT
GCTTTTGATCGATTGGATGAAATTGGACCAGTTGGAAATAAATATAATATTTGGGTTCAT
GTTGATGCTGCTTATGCTGGAAGTGCTTTCATTTGCCCTGAATATCGTCATCTCATGGCA
GGTGTTGAAACTGCAGACTCATTCAACTTTAATCCACATAAATGGATGCTTGTCAACTTT
GATTGCAGTGCAATGTGGCTTAAAGATCCTAATTGGGTTGTAAATGCTTTTAATGTTGAT
CCCTTGTACTTAAAACATGATCAACAAGGATCTGCTCCCGATTATCGTCATTGGCAAATT
CCTCTTGGAAGAAGATTCAGATCATTAAAGCTTTGGTTCGTTCTTCGACTTTATGGCATT
GAAAACTTACAAGCACATATTCGAAGACACATTGGTTTCGCACAACAATTTGAAACAAGT
TGCCGTTCTGATGAACGTTTTGAAATTGTCACAAAAGTTCAAATGGGTCTCGTTTGTTTC
CGTCTCAAAGGTTCTAATGAATTAAATGAAACACTTCTTAAAAGAATCAACGGACGTGGT
AAAATTCATCTTGTTCCATCAAAAATTAATGACACATACTTTTTGCGAATGGCTGTCTGC
TCACGTTTTACACAACCTGAAGATATGGACTTCTCATGGAATGAAGTCAGTGAGGCTGCA
ACTGAAGTTTTGAAAGAACAACAAAAGTAA

>g5265.t1 Gene=g5265 Length=489
MANKKSLESIDMEAPEFKDFAKSMVDYIANYLENIRDRPVLPSVQPGYLEKLIPSEAPSK
PESWTDVMADIERVIMPGVTHWHSPRFHAYFPTANSYPAIVADMLSGAIACIGFTWIASP
ACTELEVVMMDWLGKMIGLPAEFLACSGGKGGGVIQGTASEATLVGLLGAKAKMMQRMKA
EHPDWDDNTIVSKLVAYCSNQAHSSVERAGLLGGVQMRSLKADDNLQLRGETLEEAIKKD
LADGLIPFYVVATLGTTNSCAFDRLDEIGPVGNKYNIWVHVDAAYAGSAFICPEYRHLMA
GVETADSFNFNPHKWMLVNFDCSAMWLKDPNWVVNAFNVDPLYLKHDQQGSAPDYRHWQI
PLGRRFRSLKLWFVLRLYGIENLQAHIRRHIGFAQQFETSCRSDERFEIVTKVQMGLVCF
RLKGSNELNETLLKRINGRGKIHLVPSKINDTYFLRMAVCSRFTQPEDMDFSWNEVSEAA
TEVLKEQQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g5265.t1 CDD cd06450 DOPA_deC_like 87 479 6.93808E-136
16 g5265.t1 Gene3D G3DSA:1.20.1340.10 dopa decarboxylase 12 92 4.6E-37
17 g5265.t1 Gene3D G3DSA:3.40.640.10 - 93 388 1.8E-122
15 g5265.t1 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 389 489 2.1E-36
2 g5265.t1 PANTHER PTHR11999 GROUP II PYRIDOXAL-5-PHOSPHATE DECARBOXYLASE 12 487 2.9E-223
3 g5265.t1 PANTHER PTHR11999:SF68 HISTIDINE DECARBOXYLASE 12 487 2.9E-223
12 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 17 36 2.6E-89
7 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 40 57 2.6E-89
8 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 58 77 2.6E-89
5 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 84 103 2.6E-89
4 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 105 123 2.6E-89
9 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 124 143 2.6E-89
10 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 151 171 2.6E-89
6 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 361 376 2.6E-89
11 g5265.t1 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 404 423 2.6E-89
1 g5265.t1 Pfam PF00282 Pyridoxal-dependent decarboxylase conserved domain 46 423 2.0E-170
14 g5265.t1 ProSitePatterns PS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. 307 328 -
13 g5265.t1 SUPERFAMILY SSF53383 PLP-dependent transferases 12 483 3.02E-155

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5265/g5265.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5265.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