General information for g17804.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histidine decarboxylase.
Parent gene
- The parent gene g17804 is located on HiC_scaffold_373: 36072..41343 (+ 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 |
|---|---|---|---|---|---|---|
| HiC_scaffold_373 | g17804 | g17804.t1 | isoform | g17804.t1 | 36072 | 41343 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon1 | 36072 | 36080 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS1 | 36072 | 36080 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon2 | 36790 | 36805 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS2 | 36790 | 36805 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon3 | 36873 | 37086 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS3 | 36873 | 37086 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon4 | 38376 | 38466 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS4 | 38376 | 38466 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon5 | 38530 | 38707 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS5 | 38530 | 38707 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon6 | 39043 | 39089 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS6 | 39043 | 39089 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon7 | 39163 | 39364 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS7 | 39163 | 39364 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon8 | 39524 | 39669 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS8 | 39524 | 39669 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon9 | 39736 | 39907 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS9 | 39736 | 39907 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon10 | 40169 | 40272 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS10 | 40169 | 40272 |
| HiC_scaffold_373 | g17804 | g17804.t1 | exon | g17804.t1.exon11 | 40576 | 41343 |
| HiC_scaffold_373 | g17804 | g17804.t1 | cds | g17804.t1.CDS11 | 40576 | 41343 |
| HiC_scaffold_373 | g17804 | g17804.t1 | TSS | g17804.t1 | NA | NA |
| HiC_scaffold_373 | g17804 | g17804.t1 | TTS | g17804.t1 | NA | NA |
Sequences
>g17804.t1 Gene=g17804 Length=1947
ATGTCAAATGTTTGCTGTACTCTTGGAACAACTGGTGCTTGCGCATTTGATAATCTTGAT
GAAATTGGTGATGTTTGTCGTTCATTTGATTTGTGGCTTCACATTGATTCTGCTTATGCT
GGTTCAGCGTTTATTTGTCCTGAATTTAGAGTATGGATGAGAGGAATTGAAAAAGCTGAT
TCAATTGCATTTAATCCATCAAAATGGCTCATGGTTCATTTCGATTGCACTGCATTATGG
GTAACAAACAGCGCCGCTCTTCATCGTACATTCAATGTCGAGCCATTATATTTACAGCAT
GAGAATTCTGGATTAGCAATTGATTACATGCATTGGCAAATTCCACTCAGCAAGAGATTT
CGAGCAATAAAACTTTGGTTTGTGATAAGAAATTATGGAGTGAAAGGTTTACAAAAGCAC
ATTCGAGAAGGTGTTAGATTGGCACAAAAGTTTGAAGCTCTTGTGTTGGCTGATAATCGA
TTTGAAATTCCTGCTACAAGACATTTGGGAATGGTCGTATTTAGATTAAAAGGAGAAAAT
GAATTAACTGAAAAGCTTCTCAAGAGATTAAATCATCGTGGCAATCTTCACGCTGTTCCA
GCATCGCTGAAAGGCAAATATGTTATACGTTTCACAGTTACTTCAACTCATACAACAAAT
GATGACATAATCAAGGATTGGAATGAAATAAGAAGTGTCGCAAGTGAAATTTTGGATGAA
TGCAGCATTAAAATTGATAAACGAGTTTTGCTTAAAGATACACGTGAGAAAAACGAAGCA
TTTGGTTCAAGTCTTTTACTGGCCAATTCACCAATGTCACCAAAAGTTGTTAACGGTAGT
TTTGCGGCAATCATCGATGCTGATGAATTTTTGGCAAAAGCATATGCTGGCATCAGAATT
GCTAATCAAGATTCGCCAGCAATGAGAAGGCGTGTTCGTGGCATTTTAATGAGTGGAAGA
CAATTTTCTCTTGACAGTCGAATGGACTTGGCAATTCAAGGTATTGAGCCGACTAAGGTA
AATAACGGCGCTCAACAAGCAATCGATGAGAGTGAAGAACAAAGTTGCCAGGAAGATTAT
GAATACACGCTACTCCAGATGATGAATCTGAGCCAACAAAGATCCATCAGCCTGGACGTC
GCTGCGACTCATCACAAAGTACTTAATAATTGTAGGGAGGATCGCAAGTCATTGCCACCA
TTATCATCACACTATGACATCATTAATAGGTCACAACAGCAACACAGAAATTCATTACCA
ACAAATCTCAGCAGCAGTATCAACTATAGCAATAACAACACCATTACTAGCAACTCATTT
CAATCAAGTTTAAATATCATTGATGAAAATAAATCAATTGATGAATTCAATGACTTTAAT
TTTACTAAAAAAAGCTGCACTGAAGATTTTTCAAATTATTTATCTGATAAACGACAATCT
GAACCAGCCATTCGATTTTCGTTTTATAATAAACTATTTGACATCGATGGAACATCGCGA
ATTTCACCAACAAAAGACTATCGGAAGTTTTCATTGCCATTAGCTATGACATCGTCAACA
CTTGAGCAACCAATATCGTCTGTCAATGAACCGTCATGGAAAAGCTTTCAAAATCCAATA
AAAAAACCACAACAAACTCAGCAGCGAGTGAAATTTCATATGATAATAAACAATGAAAGC
GGTGAAAAAATTCATTCTGGATCTTCATTTGAATCGCCATCATTTAATGTTGACATTGAT
GACAAAAGTTTATTTAATGATGGAGAAAATAGTTTGAAAGGAAATGAATTTGAGAACAAT
TTTAGTGATGAAAATTTTATTAAAAGGAAATATTTTAATAACAGTGATGACAATGATGAA
AGCAATTTGAAGAATTTAAGAAAAATTTGTAAAAAATGTGGCCATGATATTCACAACAAG
AAACATAAGAGCAAAGACCAAATTTAA
>g17804.t1 Gene=g17804 Length=648
MSNVCCTLGTTGACAFDNLDEIGDVCRSFDLWLHIDSAYAGSAFICPEFRVWMRGIEKAD
SIAFNPSKWLMVHFDCTALWVTNSAALHRTFNVEPLYLQHENSGLAIDYMHWQIPLSKRF
RAIKLWFVIRNYGVKGLQKHIREGVRLAQKFEALVLADNRFEIPATRHLGMVVFRLKGEN
ELTEKLLKRLNHRGNLHAVPASLKGKYVIRFTVTSTHTTNDDIIKDWNEIRSVASEILDE
CSIKIDKRVLLKDTREKNEAFGSSLLLANSPMSPKVVNGSFAAIIDADEFLAKAYAGIRI
ANQDSPAMRRRVRGILMSGRQFSLDSRMDLAIQGIEPTKVNNGAQQAIDESEEQSCQEDY
EYTLLQMMNLSQQRSISLDVAATHHKVLNNCREDRKSLPPLSSHYDIINRSQQQHRNSLP
TNLSSSINYSNNNTITSNSFQSSLNIIDENKSIDEFNDFNFTKKSCTEDFSNYLSDKRQS
EPAIRFSFYNKLFDIDGTSRISPTKDYRKFSLPLAMTSSTLEQPISSVNEPSWKSFQNPI
KKPQQTQQRVKFHMIINNESGEKIHSGSSFESPSFNVDIDDKSLFNDGENSLKGNEFENN
FSDENFIKRKYFNNSDDNDESNLKNLRKICKKCGHDIHNKKHKSKDQI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g17804.t1 | Gene3D | G3DSA:3.40.640.10 | - | 2 | 142 | 0 |
| 7 | g17804.t1 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 143 | 240 | 0 |
| 2 | g17804.t1 | PANTHER | PTHR11999 | GROUP II PYRIDOXAL-5-PHOSPHATE DECARBOXYLASE | 3 | 342 | 0 |
| 3 | g17804.t1 | PANTHER | PTHR11999:SF68 | HISTIDINE DECARBOXYLASE | 3 | 342 | 0 |
| 5 | g17804.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 115 | 130 | 0 |
| 4 | g17804.t1 | PRINTS | PR00800 | Aromatic-L-amino-acid decarboxylase signature | 158 | 177 | 0 |
| 1 | g17804.t1 | Pfam | PF00282 | Pyridoxal-dependent decarboxylase conserved domain | 4 | 177 | 0 |
| 6 | g17804.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 4 | 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 transcript has been annotated with K01590 (histidine decarboxylase)
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. There were no conditions that were differentially expressed