General information for g16330.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ornithine decarboxylase.
Parent gene
- The parent gene g16330 is located on chr_4: 9094296..9094640 (+ 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_4 | g16330 | g16330.t1 | isoform | g16330.t1 | 9094296 | 9094640 |
| chr_4 | g16330 | g16330.t1 | exon | g16330.t1.exon1 | 9094296 | 9094640 |
| chr_4 | g16330 | g16330.t1 | cds | g16330.t1.CDS1 | 9094296 | 9094640 |
| chr_4 | g16330 | g16330.t1 | TSS | g16330.t1 | NA | NA |
| chr_4 | g16330 | g16330.t1 | TTS | g16330.t1 | NA | NA |
Sequences
>g16330.t1 Gene=g16330 Length=345
ATGAGTAAAATTTTTAATTATTTTTCTCACTTTCATTTAGAAAAATCCATTGAAAGATCA
TTGAAAGTTGAGAATGATTCGCATTATATTTGCAATTTGAGTGATCTTATTCGAAAATAT
GAAGATTGGAAAACTTATTTGCCACGAGTTAAACCATATTATGCAGTAAAATGCAATGAC
AATATTAACGTTCTCAAACTATTAGCATTTATTGGTTGCTCATTTGATTGTGCATCAGCA
GGCGAGATTGAGAAAATTTTATCATTAAACGTCGGTCCAGAACGAATTATTTTTGCAAAT
ACAACGAAATTTGCAAAAGCATATCGAATTTGCAGAACGTCATAA
>g16330.t1 Gene=g16330 Length=114
MSKIFNYFSHFHLEKSIERSLKVENDSHYICNLSDLIRKYEDWKTYLPRVKPYYAVKCND
NINVLKLLAFIGCSFDCASAGEIEKILSLNVGPERIIFANTTKFAKAYRICRTS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g16330.t1 | Gene3D | G3DSA:3.20.20.10 | Alanine racemase | 34 | 114 | 3.5E-24 |
| 2 | g16330.t1 | PANTHER | PTHR11482 | ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE | 17 | 106 | 3.8E-30 |
| 3 | g16330.t1 | PANTHER | PTHR11482:SF6 | ORNITHINE DECARBOXYLASE 1-RELATED | 17 | 106 | 3.8E-30 |
| 4 | g16330.t1 | PRINTS | PR01182 | Ornithine decarboxylase signature | 26 | 50 | 1.8E-19 |
| 6 | g16330.t1 | PRINTS | PR01182 | Ornithine decarboxylase signature | 52 | 79 | 1.8E-19 |
| 7 | g16330.t1 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 54 | 72 | 8.8E-9 |
| 8 | g16330.t1 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 74 | 86 | 8.8E-9 |
| 5 | g16330.t1 | PRINTS | PR01182 | Ornithine decarboxylase signature | 96 | 114 | 1.8E-19 |
| 1 | g16330.t1 | Pfam | PF02784 | Pyridoxal-dependent decarboxylase, pyridoxal binding domain | 34 | 106 | 2.5E-22 |
| 10 | g16330.t1 | ProSitePatterns | PS00878 | Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. | 54 | 72 | - |
| 9 | g16330.t1 | SUPERFAMILY | SSF51419 | PLP-binding barrel | 28 | 109 | 9.35E-20 |
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:0003824 | catalytic activity | MF |
| GO:0006596 | polyamine biosynthetic process | BP |
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