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.t4 isoform g5265.t4 8311058 8314233
chr_2 g5265 g5265.t4 exon g5265.t4.exon1 8311058 8311176
chr_2 g5265 g5265.t4 TSS g5265.t4 8311072 8311072
chr_2 g5265 g5265.t4 exon g5265.t4.exon2 8311720 8311805
chr_2 g5265 g5265.t4 cds g5265.t4.CDS1 8311726 8311805
chr_2 g5265 g5265.t4 exon g5265.t4.exon3 8312673 8312817
chr_2 g5265 g5265.t4 cds g5265.t4.CDS2 8312673 8312817
chr_2 g5265 g5265.t4 exon g5265.t4.exon4 8312897 8313236
chr_2 g5265 g5265.t4 cds g5265.t4.CDS3 8312897 8313236
chr_2 g5265 g5265.t4 exon g5265.t4.exon5 8313297 8313850
chr_2 g5265 g5265.t4 cds g5265.t4.CDS4 8313297 8313850
chr_2 g5265 g5265.t4 exon g5265.t4.exon6 8313916 8314233
chr_2 g5265 g5265.t4 cds g5265.t4.CDS5 8313916 8314233
chr_2 g5265 g5265.t4 TTS g5265.t4 8314346 8314346

Sequences

>g5265.t4 Gene=g5265 Length=1562
ATCAACATAAAGCTTAGTTACTTTTTAGCTGTTGTACGCTTCGTTTCGTTAGTGTATCTT
TGTCGTTTTATAATTTTTTTTATTCATCTCACGACTTTAAATTTGTCCCATTAAAGCAAA
TCGACATGGAAGCACCTGAGTTTAAAGACTTTGCCAAGTCAATGGTTGACTATATCGCAA
ACTATCTGGAGAATATTCGTGATAGGCCAGTTTTGCCATCAGTTCAACCAGGTTATTTAG
AAAAATTAATTCCATCTGAAGCTCCCTCAAAACCAGAAAGTTGGACTGATGTTATGGCAG
ATATTGAAAGAGTTATCATGCCTGGTGTGACTCATTGGCATTCGCCTAGATTTCATGCAT
ATTTCCCAACCGCAAATTCTTACCCAGCTATTGTTGCTGATATGTTAAGTGGTGCGATCG
CTTGTATTGGTTTCACATGGATTGCTAGTCCGGCATGTACTGAATTAGAAGTTGTCATGA
TGGATTGGCTAGGAAAAATGATTGGTTTGCCAGCAGAATTTCTTGCATGTTCAGGTGGAA
AAGGTGGCGGTGTTATACAAGGAACAGCTAGTGAAGCTACACTTGTTGGTTTATTAGGTG
CAAAAGCAAAAATGATGCAGCGAATGAAAGCGGAACATCCAGATTGGGATGATAATACAA
TTGTCTCAAAATTGGTCGCTTATTGCTCAAATCAAGCACATTCATCAGTTGAAAGAGCTG
GTCTATTGGGAGGCGTGCAAATGAGAAGTTTGAAAGCTGATGATAATTTGCAATTGAGAG
GCGAAACATTAGAAGAAGCGATTAAAAAAGATTTAGCTGATGGTTTAATTCCATTTTATG
TGGTTGCAACATTGGGTACAACGAACTCTTGTGCTTTTGATCGATTGGATGAAATTGGAC
CAGTTGGAAATAAATATAATATTTGGGTTCATGTTGATGCTGCTTATGCTGGAAGTGCTT
TCATTTGCCCTGAATATCGTCATCTCATGGCAGGTGTTGAAACTGCAGACTCATTCAACT
TTAATCCACATAAATGGATGCTTGTCAACTTTGATTGCAGTGCAATGTGGCTTAAAGATC
CTAATTGGGTTGTAAATGCTTTTAATGTTGATCCCTTGTACTTAAAACATGATCAACAAG
GATCTGCTCCCGATTATCGTCATTGGCAAATTCCTCTTGGAAGAAGATTCAGATCATTAA
AGCTTTGGTTCGTTCTTCGACTTTATGGCATTGAAAACTTACAAGCACATATTCGAAGAC
ACATTGGTTTCGCACAACAATTTGAAACAAGTTGCCGTTCTGATGAACGTTTTGAAATTG
TCACAAAAGTTCAAATGGGTCTCGTTTGTTTCCGTCTCAAAGGTTCTAATGAATTAAATG
AAACACTTCTTAAAAGAATCAACGGACGTGGTAAAATTCATCTTGTTCCATCAAAAATTA
ATGACACATACTTTTTGCGAATGGCTGTCTGCTCACGTTTTACACAACCTGAAGATATGG
ACTTCTCATGGAATGAAGTCAGTGAGGCTGCAACTGAAGTTTTGAAAGAACAACAAAAGT
AA

>g5265.t4 Gene=g5265 Length=478
MEAPEFKDFAKSMVDYIANYLENIRDRPVLPSVQPGYLEKLIPSEAPSKPESWTDVMADI
ERVIMPGVTHWHSPRFHAYFPTANSYPAIVADMLSGAIACIGFTWIASPACTELEVVMMD
WLGKMIGLPAEFLACSGGKGGGVIQGTASEATLVGLLGAKAKMMQRMKAEHPDWDDNTIV
SKLVAYCSNQAHSSVERAGLLGGVQMRSLKADDNLQLRGETLEEAIKKDLADGLIPFYVV
ATLGTTNSCAFDRLDEIGPVGNKYNIWVHVDAAYAGSAFICPEYRHLMAGVETADSFNFN
PHKWMLVNFDCSAMWLKDPNWVVNAFNVDPLYLKHDQQGSAPDYRHWQIPLGRRFRSLKL
WFVLRLYGIENLQAHIRRHIGFAQQFETSCRSDERFEIVTKVQMGLVCFRLKGSNELNET
LLKRINGRGKIHLVPSKINDTYFLRMAVCSRFTQPEDMDFSWNEVSEAATEVLKEQQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g5265.t4 CDD cd06450 DOPA_deC_like 76 468 5.25456E-136
16 g5265.t4 Gene3D G3DSA:1.20.1340.10 dopa decarboxylase 1 81 4.4E-37
17 g5265.t4 Gene3D G3DSA:3.40.640.10 - 82 377 1.7E-122
15 g5265.t4 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 378 478 2.0E-36
2 g5265.t4 PANTHER PTHR11999 GROUP II PYRIDOXAL-5-PHOSPHATE DECARBOXYLASE 1 476 2.8E-223
3 g5265.t4 PANTHER PTHR11999:SF68 HISTIDINE DECARBOXYLASE 1 476 2.8E-223
5 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 6 25 2.2E-89
12 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 29 46 2.2E-89
4 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 47 66 2.2E-89
7 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 73 92 2.2E-89
8 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 94 112 2.2E-89
6 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 113 132 2.2E-89
9 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 140 160 2.2E-89
11 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 350 365 2.2E-89
10 g5265.t4 PRINTS PR00800 Aromatic-L-amino-acid decarboxylase signature 393 412 2.2E-89
1 g5265.t4 Pfam PF00282 Pyridoxal-dependent decarboxylase conserved domain 35 412 1.9E-170
14 g5265.t4 ProSitePatterns PS00392 DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. 296 317 -
13 g5265.t4 SUPERFAMILY SSF53383 PLP-dependent transferases 1 472 2.95E-155

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5265/g5265.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5265.t4.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