General information for g4890.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ornithine decarboxylase 1.
Parent gene
- The parent gene g4890 is located on chr_2: 5824055..5825202 (- 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 | g4890 | g4890.t3 | isoform | g4890.t3 | 5823105 | 5825202 |
| chr_2 | g4890 | g4890.t3 | exon | g4890.t3.exon1 | 5823105 | 5823501 |
| chr_2 | g4890 | g4890.t3 | TTS | g4890.t3 | 5823116 | 5823116 |
| chr_2 | g4890 | g4890.t3 | cds | g4890.t3.CDS1 | 5823450 | 5823501 |
| chr_2 | g4890 | g4890.t3 | exon | g4890.t3.exon2 | 5823588 | 5823977 |
| chr_2 | g4890 | g4890.t3 | cds | g4890.t3.CDS2 | 5823588 | 5823977 |
| chr_2 | g4890 | g4890.t3 | exon | g4890.t3.exon3 | 5824042 | 5824165 |
| chr_2 | g4890 | g4890.t3 | cds | g4890.t3.CDS3 | 5824042 | 5824118 |
| chr_2 | g4890 | g4890.t3 | exon | g4890.t3.exon4 | 5824226 | 5824482 |
| chr_2 | g4890 | g4890.t3 | exon | g4890.t3.exon5 | 5824786 | 5825202 |
| chr_2 | g4890 | g4890.t3 | TSS | g4890.t3 | 5825239 | 5825239 |
Sequences
>g4890.t3 Gene=g4890 Length=1585
ATGAGTAAAGTTTTTAAATTTTTGTCCCACTTTCATTTAGAAAAATCAATTGAACGATCA
TTAAAAGTCGTGAATGATTCGCATTATATTTGCAATTTGAGTGATGTTATTCGAAAATAT
GAAGATTGGAAAACTCATTTGCCACGAGTGCGACCACATTATGCAGTAAAATGCAATGAC
AATATTAATGTTCTCAAAACTTTAGCATCTATTGGTTGCTCATTTGATTGTGCGTCAGCA
GGCGAGATTGAGAAAATTTTATCATTAAATGTCAATCCAGAACGAATTATTTTTGCAAAT
ACAACAAAATTTGCAAAGCATATCGAGTTTGCAGAACAAAATCAAGTGAACATCATGACG
TTTGATAATGAAGATGAACTTTATAAAATCCTTAAAATTCATCCAAGCGCAAAGTAATTT
AGTTTTGAGAATACGCTATAGCTCAGATAAGGCAATTTACAAATTGGGCAAAAAGTTTGG
ATCTTTACCAAATACGGAAGCTCCTGAGTTGCTTAAATTAGCCAAAAGTTTAAATCTTAA
TGTCATTGGCATCAGTTTTCATATCGGTTCAAGCTGTGAAGATTATGAGGTTTATTGTGG
AGCAATTGCAATTTCTAGAGTTTTATTTCAATTTGCTGCTGACATTGGCTATAACTTTAG
AATCCTTGATATCGGTGGCTTTCCAGGAGATAATTTCAATCGAGTCAAAGAGTTTTCATG
CATGATTAATAATGCATTGAATCAAAATTTTCCACTCAATGAATTTCCTAATCTGGAAAT
TTTATCTGAACCGGGAAGATATTTCGTTGAATCTGCTTTTACTCTCGTCACTCAAATTCA
TTCACGAAAAATCACAAGAGATGCAGATGGGAAAATTGTTGATGTGATGTATTATCTAAA
TGAAGGAGTTTACTCAAATTTCCTTTTCATACCACTCGGTCCTGAAGAAGTAATACCAAA
AATTCTTTCACATAAACGTACGAATGAGCAATTTAGAAGCACGATTTGGGGTCCGACATG
CGATTCAACTGACAAAATTTGTGAGGACATTAAATTAGAATTGCTAGAAATTGGTGATGT
TATTTATTTCACTAATATGGGAGCTTACACAATTCCTTTGAGTACAAGCTTCAATGGTTT
CCCAACAACAAAAATTGTTTACTTCTTGGAAGAGAATGTCGTTGATAGCAACAAATTAAA
CACTGAAATGTTTGATTTTAACTTCATCAACGACGCATGATGATGCAAAATTTGATTGAA
ATTTCATGTATTTAAATATTTGTGCACGCGAGGGCTGACTATGTAAAGAATATTTGCAAA
CTAAACTAATTACCTAATTGATTATTTGTGAGATAGAACTTTATTGTTTAATATTTTATT
TTCACATGCAATAGTTTTAATTTATTACAAATTTATTTTGTACACGATGTGTTGGTAGAA
GTTCTTTCTTTTTGTTAACTCATGACATTTCCACAATTTAATTAAAAGTAATTCTTTTCC
ATTTGTGAAACAGTTCTTTTGCTTTGTTGACTACATTTCCTTTAGAAAAATAAAGATAAT
AAAGTTAATTAGAAAATATCACAGA
>g4890.t3 Gene=g4890 Length=172
MINNALNQNFPLNEFPNLEILSEPGRYFVESAFTLVTQIHSRKITRDADGKIVDVMYYLN
EGVYSNFLFIPLGPEEVIPKILSHKRTNEQFRSTIWGPTCDSTDKICEDIKLELLEIGDV
IYFTNMGAYTIPLSTSFNGFPTTKIVYFLEENVVDSNKLNTEMFDFNFINDA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4890.t3 | Gene3D | G3DSA:2.40.37.10 | Lyase | 1 | 160 | 0 |
| 2 | g4890.t3 | PANTHER | PTHR11482 | ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE | 2 | 152 | 0 |
| 3 | g4890.t3 | PANTHER | PTHR11482:SF6 | ORNITHINE DECARBOXYLASE 1-RELATED | 2 | 152 | 0 |
| 4 | g4890.t3 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 20 | 39 | 0 |
| 5 | g4890.t3 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 127 | 140 | 0 |
| 1 | g4890.t3 | Pfam | PF00278 | Pyridoxal-dependent decarboxylase, C-terminal sheet domain | 27 | 127 | 0 |
| 6 | g4890.t3 | SUPERFAMILY | SSF50621 | Alanine racemase C-terminal domain-like | 8 | 152 | 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: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