General information for g5265.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Aromatic-L-amino-acid decarboxylase .
Parent gene
- The parent gene g5265 is located on chr_2: 8314233..8315144 (+ strand)
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.t7 | isoform | g5265.t7 | 8313306 | 8314233 |
| chr_2 | g5265 | g5265.t7 | exon | g5265.t7.exon1 | 8313306 | 8313850 |
| chr_2 | g5265 | g5265.t7 | cds | g5265.t7.CDS1 | 8313347 | 8313850 |
| chr_2 | g5265 | g5265.t7 | exon | g5265.t7.exon2 | 8313916 | 8314233 |
| chr_2 | g5265 | g5265.t7 | cds | g5265.t7.CDS2 | 8313916 | 8314233 |
| chr_2 | g5265 | g5265.t7 | TTS | g5265.t7 | 8314346 | 8314346 |
| chr_2 | g5265 | g5265.t7 | TSS | g5265.t7 | NA | NA |
Sequences
>g5265.t7 Gene=g5265 Length=863
ATTCATCAGTTGAAAGAGCTGGTCTATTGGGAGGCGTGCAAATGAGAAGTTTGAAAGCTG
ATGATAATTTGCAATTGAGAGGCGAAACATTAGAAGAAGCGATTAAAAAAGATTTAGCTG
ATGGTTTAATTCCATTTTATGTGGTTGCAACATTGGGTACAACGAACTCTTGTGCTTTTG
ATCGATTGGATGAAATTGGACCAGTTGGAAATAAATATAATATTTGGGTTCATGTTGATG
CTGCTTATGCTGGAAGTGCTTTCATTTGCCCTGAATATCGTCATCTCATGGCAGGTGTTG
AAACTGCAGACTCATTCAACTTTAATCCACATAAATGGATGCTTGTCAACTTTGATTGCA
GTGCAATGTGGCTTAAAGATCCTAATTGGGTTGTAAATGCTTTTAATGTTGATCCCTTGT
ACTTAAAACATGATCAACAAGGATCTGCTCCCGATTATCGTCATTGGCAAATTCCTCTTG
GAAGAAGATTCAGATCATTAAAGCTTTGGTTCGTTCTTCGACTTTATGGCATTGAAAACT
TACAAGCACATATTCGAAGACACATTGGTTTCGCACAACAATTTGAAACAAGTTGCCGTT
CTGATGAACGTTTTGAAATTGTCACAAAAGTTCAAATGGGTCTCGTTTGTTTCCGTCTCA
AAGGTTCTAATGAATTAAATGAAACACTTCTTAAAAGAATCAACGGACGTGGTAAAATTC
ATCTTGTTCCATCAAAAATTAATGACACATACTTTTTGCGAATGGCTGTCTGCTCACGTT
TTACACAACCTGAAGATATGGACTTCTCATGGAATGAAGTCAGTGAGGCTGCAACTGAAG
TTTTGAAAGAACAACAAAAGTAA
>g5265.t7 Gene=g5265 Length=273
MRSLKADDNLQLRGETLEEAIKKDLADGLIPFYVVATLGTTNSCAFDRLDEIGPVGNKYN
IWVHVDAAYAGSAFICPEYRHLMAGVETADSFNFNPHKWMLVNFDCSAMWLKDPNWVVNA
FNVDPLYLKHDQQGSAPDYRHWQIPLGRRFRSLKLWFVLRLYGIENLQAHIRRHIGFAQQ
FETSCRSDERFEIVTKVQMGLVCFRLKGSNELNETLLKRINGRGKIHLVPSKINDTYFLR
MAVCSRFTQPEDMDFSWNEVSEAATEVLKEQQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5265.t7 | Gene3D | G3DSA:3.40.640.10 | - | 1 | 172 | 3.3E-77 |
| 8 | g5265.t7 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 173 | 273 | 6.9E-37 |
| 2 | g5265.t7 | PANTHER | PTHR11999 | GROUP II PYRIDOXAL-5-PHOSPHATE DECARBOXYLASE | 1 | 268 | 5.0E-122 |
| 3 | g5265.t7 | PANTHER | PTHR11999:SF60 | 3,4-DIHYDROXYPHENYLACETALDEHYDE SYNTHASE | 1 | 268 | 5.0E-122 |
| 5 | g5265.t7 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 145 | 160 | 2.6E-15 |
| 4 | g5265.t7 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 188 | 207 | 2.6E-15 |
| 1 | g5265.t7 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 1 | 207 | 8.4E-95 |
| 7 | g5265.t7 | ProSitePatterns | PS00392 | DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. | 91 | 112 | - |
| 6 | g5265.t7 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 2 | 267 | 6.39E-89 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5265/g5265.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5265.t7.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.
