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.t2 isoform g5265.t2 8311058 8313837
chr_2 g5265 g5265.t2 exon g5265.t2.exon1 8311058 8311176
chr_2 g5265 g5265.t2 TSS g5265.t2 8311072 8311072
chr_2 g5265 g5265.t2 exon g5265.t2.exon2 8311499 8311550
chr_2 g5265 g5265.t2 cds g5265.t2.CDS1 8311524 8311550
chr_2 g5265 g5265.t2 exon g5265.t2.exon3 8311720 8311805
chr_2 g5265 g5265.t2 cds g5265.t2.CDS2 8311720 8311805
chr_2 g5265 g5265.t2 exon g5265.t2.exon4 8312673 8312817
chr_2 g5265 g5265.t2 cds g5265.t2.CDS3 8312673 8312817
chr_2 g5265 g5265.t2 exon g5265.t2.exon5 8312897 8313236
chr_2 g5265 g5265.t2 cds g5265.t2.CDS4 8312897 8313236
chr_2 g5265 g5265.t2 exon g5265.t2.exon6 8313297 8313837
chr_2 g5265 g5265.t2 cds g5265.t2.CDS5 8313297 8313835
chr_2 g5265 g5265.t2 TTS g5265.t2 8314346 8314346

Sequences

>g5265.t2 Gene=g5265 Length=1283
ATCAACATAAAGCTTAGTTACTTTTTAGCTGTTGTACGCTTCGTTTCGTTAGTGTATCTT
TGTCGTTTTATAATTTTTTTTATTCATCTCACGACTTTAAATTTGTCCCATTAAAGCAAA
ATTTAACTACACTTGTATCTAAAAATGGCTAACAAAAAATCATTGGAATCTATCGACATG
GAAGCACCTGAGTTTAAAGACTTTGCCAAGTCAATGGTTGACTATATCGCAAACTATCTG
GAGAATATTCGTGATAGGCCAGTTTTGCCATCAGTTCAACCAGGTTATTTAGAAAAATTA
ATTCCATCTGAAGCTCCCTCAAAACCAGAAAGTTGGACTGATGTTATGGCAGATATTGAA
AGAGTTATCATGCCTGGTGTGACTCATTGGCATTCGCCTAGATTTCATGCATATTTCCCA
ACCGCAAATTCTTACCCAGCTATTGTTGCTGATATGTTAAGTGGTGCGATCGCTTGTATT
GGTTTCACATGGATTGCTAGTCCGGCATGTACTGAATTAGAAGTTGTCATGATGGATTGG
CTAGGAAAAATGATTGGTTTGCCAGCAGAATTTCTTGCATGTTCAGGTGGAAAAGGTGGC
GGTGTTATACAAGGAACAGCTAGTGAAGCTACACTTGTTGGTTTATTAGGTGCAAAAGCA
AAAATGATGCAGCGAATGAAAGCGGAACATCCAGATTGGGATGATAATACAATTGTCTCA
AAATTGGTCGCTTATTGCTCAAATCAAGCACATTCATCAGTTGAAAGAGCTGGTCTATTG
GGAGGCGTGCAAATGAGAAGTTTGAAAGCTGATGATAATTTGCAATTGAGAGGCGAAACA
TTAGAAGAAGCGATTAAAAAAGATTTAGCTGATGGTTTAATTCCATTTTATGTGGTTGCA
ACATTGGGTACAACGAACTCTTGTGCTTTTGATCGATTGGATGAAATTGGACCAGTTGGA
AATAAATATAATATTTGGGTTCATGTTGATGCTGCTTATGCTGGAAGTGCTTTCATTTGC
CCTGAATATCGTCATCTCATGGCAGGTGTTGAAACTGCAGACTCATTCAACTTTAATCCA
CATAAATGGATGCTTGTCAACTTTGATTGCAGTGCAATGTGGCTTAAAGATCCTAATTGG
GTTGTAAATGCTTTTAATGTTGATCCCTTGTACTTAAAACATGATCAACAAGGATCTGCT
CCCGATTATCGTCATTGGCAAATTCCTCTTGGAAGAAGATTCAGATCATTAAAGCTTTGG
TTCGTTCTTCGACTTTATGGCAT

>g5265.t2 Gene=g5265 Length=379
MANKKSLESIDMEAPEFKDFAKSMVDYIANYLENIRDRPVLPSVQPGYLEKLIPSEAPSK
PESWTDVMADIERVIMPGVTHWHSPRFHAYFPTANSYPAIVADMLSGAIACIGFTWIASP
ACTELEVVMMDWLGKMIGLPAEFLACSGGKGGGVIQGTASEATLVGLLGAKAKMMQRMKA
EHPDWDDNTIVSKLVAYCSNQAHSSVERAGLLGGVQMRSLKADDNLQLRGETLEEAIKKD
LADGLIPFYVVATLGTTNSCAFDRLDEIGPVGNKYNIWVHVDAAYAGSAFICPEYRHLMA
GVETADSFNFNPHKWMLVNFDCSAMWLKDPNWVVNAFNVDPLYLKHDQQGSAPDYRHWQI
PLGRRFRSLKLWFVLRLYG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g5265.t2 Gene3D G3DSA:1.20.1340.10 dopa decarboxylase 12 92 3.0E-37
15 g5265.t2 Gene3D G3DSA:3.40.640.10 - 93 379 1.5E-118
2 g5265.t2 PANTHER PTHR11999 GROUP II PYRIDOXAL-5-PHOSPHATE DECARBOXYLASE 12 379 4.8E-184
3 g5265.t2 PANTHER PTHR11999:SF68 HISTIDINE DECARBOXYLASE 12 379 4.8E-184
11 g5265.t2 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 17 36 5.2E-79
7 g5265.t2 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 40 57 5.2E-79
8 g5265.t2 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 58 77 5.2E-79
5 g5265.t2 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 84 103 5.2E-79
4 g5265.t2 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 105 123 5.2E-79
9 g5265.t2 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 124 143 5.2E-79
10 g5265.t2 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 151 171 5.2E-79
6 g5265.t2 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 361 376 5.2E-79
1 g5265.t2 Pfam PF00282 Pyridoxal-dependent decarboxylase conserved domain 46 379 1.2E-151
13 g5265.t2 ProSitePatterns PS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. 307 328 -
12 g5265.t2 SUPERFAMILY SSF53383 PLP-dependent transferases 12 379 6.83E-127

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5265/g5265.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5265.t2.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

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.

Raw TPM values