General information for g12450.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histidine decarboxylase.
Parent gene
- The parent gene g12450 is located on chr_1: 23795140..23797173 (+ 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_1 | g12450 | g12450.t1 | isoform | g12450.t1 | 23795140 | 23797173 |
| chr_1 | g12450 | g12450.t1 | exon | g12450.t1.exon1 | 23795140 | 23795167 |
| chr_1 | g12450 | g12450.t1 | cds | g12450.t1.CDS1 | 23795140 | 23795167 |
| chr_1 | g12450 | g12450.t1 | exon | g12450.t1.exon2 | 23795886 | 23796172 |
| chr_1 | g12450 | g12450.t1 | cds | g12450.t1.CDS2 | 23795886 | 23796172 |
| chr_1 | g12450 | g12450.t1 | exon | g12450.t1.exon3 | 23796228 | 23796372 |
| chr_1 | g12450 | g12450.t1 | cds | g12450.t1.CDS3 | 23796228 | 23796372 |
| chr_1 | g12450 | g12450.t1 | exon | g12450.t1.exon4 | 23796429 | 23796682 |
| chr_1 | g12450 | g12450.t1 | cds | g12450.t1.CDS4 | 23796429 | 23796682 |
| chr_1 | g12450 | g12450.t1 | exon | g12450.t1.exon5 | 23797147 | 23797173 |
| chr_1 | g12450 | g12450.t1 | cds | g12450.t1.CDS5 | 23797147 | 23797173 |
| chr_1 | g12450 | g12450.t1 | TSS | g12450.t1 | NA | NA |
| chr_1 | g12450 | g12450.t1 | TTS | g12450.t1 | NA | NA |
Sequences
>g12450.t1 Gene=g12450 Length=741
ATGGATGTGAATGAATACCGTAAAAGAGGAAAGGAAATGGTAGATTTTATAGCAGACTAT
TTAGAGAACATTCGAGATCGTCGTGTCTTTCCGGATGTACAGCCTGGCTATATGCGAAAT
TTATTGCCTGAATCAGCGCCAAATGATGGTGAAGATTGGTCGTCAATTTTCAACGATATC
GAACGCGTCATAATGCCTGGTGTAACACATTGGCAAAGTCCTCATATGCATGCCTATTTT
CCTGCATTAAATTCATTTCCATCGTTACTCGGCGACATGCTGGCCGATGCAATTAACTGT
CTTGGATTTACATGGGCATCATCGCCTGCATGTACTGAACTTGAAACAATCACCATGAAT
TGGCTTGGAAAGATGATTGGATTGCCAGATTCATTTTTACATAGCAAAAATGGAAGAGGT
GGTGGTGTAATACAAACTACAGCTAGTGAAGCAACATTAGTTTGCTTACTTGCTGGAAGA
ACGAAAGCGATAAGAAAATTTCACGAGCATACACCAGGATTTCAAGATGCAGAAATCAAT
GCAAGACTCGTTGCTTATTGCTCTGATCAAGCGCATTCAAGTGTAGAAAAAGCAGCTCTC
ATTGGACTCGTTAGAATGAGATTTATTGAAGCTGATGGAAATCTTGGATTACGTGGTGGT
GCATTGAAAGAAGCAATTGAAGAAGATATAAGAAATGGATTAATTCCTTTCTGGAAAAAT
GATAAAATACACACTGGTTAA
>g12450.t1 Gene=g12450 Length=246
MDVNEYRKRGKEMVDFIADYLENIRDRRVFPDVQPGYMRNLLPESAPNDGEDWSSIFNDI
ERVIMPGVTHWQSPHMHAYFPALNSFPSLLGDMLADAINCLGFTWASSPACTELETITMN
WLGKMIGLPDSFLHSKNGRGGGVIQTTASEATLVCLLAGRTKAIRKFHEHTPGFQDAEIN
ARLVAYCSDQAHSSVEKAALIGLVRMRFIEADGNLGLRGGALKEAIEEDIRNGLIPFWKN
DKIHTG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g12450.t1 | Gene3D | G3DSA:1.20.1340.10 | dopa decarboxylase | 1 | 81 | 0 |
| 13 | g12450.t1 | Gene3D | G3DSA:3.40.640.10 | - | 83 | 240 | 0 |
| 2 | g12450.t1 | PANTHER | PTHR11999 | GROUP II PYRIDOXAL-5-PHOSPHATE DECARBOXYLASE | 1 | 240 | 0 |
| 3 | g12450.t1 | PANTHER | PTHR11999:SF68 | HISTIDINE DECARBOXYLASE | 1 | 240 | 0 |
| 6 | g12450.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 6 | 25 | 0 |
| 10 | g12450.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 29 | 46 | 0 |
| 4 | g12450.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 47 | 66 | 0 |
| 8 | g12450.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 73 | 92 | 0 |
| 9 | g12450.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 94 | 112 | 0 |
| 7 | g12450.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 113 | 132 | 0 |
| 5 | g12450.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 140 | 160 | 0 |
| 1 | g12450.t1 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 35 | 239 | 0 |
| 11 | g12450.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 1 | 237 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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. There were no conditions that were differentially expressed