General information for g15886.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 g15886 is located on chr_4: 7176923..7177684 (- 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 | g15886 | g15886.t3 | TTS | g15886.t3 | 7175648 | 7175648 |
| chr_4 | g15886 | g15886.t3 | isoform | g15886.t3 | 7175673 | 7177684 |
| chr_4 | g15886 | g15886.t3 | exon | g15886.t3.exon1 | 7175673 | 7175733 |
| chr_4 | g15886 | g15886.t3 | exon | g15886.t3.exon2 | 7175801 | 7176267 |
| chr_4 | g15886 | g15886.t3 | cds | g15886.t3.CDS1 | 7176248 | 7176267 |
| chr_4 | g15886 | g15886.t3 | exon | g15886.t3.exon3 | 7176329 | 7176382 |
| chr_4 | g15886 | g15886.t3 | cds | g15886.t3.CDS2 | 7176329 | 7176382 |
| chr_4 | g15886 | g15886.t3 | exon | g15886.t3.exon4 | 7176441 | 7176682 |
| chr_4 | g15886 | g15886.t3 | cds | g15886.t3.CDS3 | 7176441 | 7176682 |
| chr_4 | g15886 | g15886.t3 | exon | g15886.t3.exon5 | 7176742 | 7176899 |
| chr_4 | g15886 | g15886.t3 | cds | g15886.t3.CDS4 | 7176742 | 7176899 |
| chr_4 | g15886 | g15886.t3 | exon | g15886.t3.exon6 | 7177184 | 7177224 |
| chr_4 | g15886 | g15886.t3 | cds | g15886.t3.CDS5 | 7177184 | 7177224 |
| chr_4 | g15886 | g15886.t3 | exon | g15886.t3.exon7 | 7177447 | 7177684 |
| chr_4 | g15886 | g15886.t3 | cds | g15886.t3.CDS6 | 7177447 | 7177684 |
| chr_4 | g15886 | g15886.t3 | TSS | g15886.t3 | 7177702 | 7177702 |
Sequences
>g15886.t3 Gene=g15886 Length=1261
ATGTCGTCAACAACACTGCCTAAAGAAACTGTTCAAATTATTGATAAATTTGATTTATTT
CAATTAGTTCATGATCGGATTAAAGAGATTGGAATTGATGAATCATTTTTCATCACAGAC
GTTGGCGATGTTGTGAAGAAATTTATTTTATGGAAAGAATTATTTCCTCGTATTGAACCT
GATTTTGCAATTAAAAGTAATAATCTTCCTGTAATTGCTTCTACTTTGGCTGCTTTAGGT
GCTGGTTTTGATTGTGCAAGTCATGGAGAGATAACACAAGTTCTTGAAATGGGTGTTGAA
CCAGAAAAAATTGTTTTTGCACAAACTGTTAAACCAATTTACAATATCAAATTGGCCAAA
GAGAAGAATGTTTTTAAAATGACTTTTGATAATGAAAATGAACTTTATAAAGTTAAGGAA
CATTTTCCAGAAGCTCATCTTCTTTTACGTCTTGGTTTTTCTCCAAAGTCATCAAATAAA
ATAGCTTTTGGTGCTAAATTTGGTTGTTCTTTTGAAACTGGCAAAGATTTATTGAAAAAG
GCAAAAGAATTAAATTTAAATGTCAAAGGAGTTGCTTTTCATATTGGTGTCGGTTGTGAA
GAATATGAAATTTTTAGAAAGGCAATTGAAGACAGCAGCAAGATGTTTGAATATGGAAAA
TCTTTGGGTTTCAATATGGATGTTCTTGATATTGGAGGCGGATTTCCTGGCCATGAAACT
AAAACAATCGTAAGTTTCAAAAGTAATCAATGAAAGCATAGAACAAAATTTTCCCGATCC
AAGTGTAAAAATAATTTCGGAGCCAGGCCAATTTTTTGCAACACATTCGATGACACTTGT
GGTAAATGTTCATTCTAAAGCTGTAAAATTAAATGAAAATGGAGAAAAAATTTTCCATTA
TTACATCACGGATGGAATTTACCAATCATTTGCAATGAAAGGAAGTGGTGGAAATAATCC
GAATCCATTGGTTGTTAAAACACTTCGGGACACGAGTGGTGACAATTTAAAGAAAAGTGT
AATTTGGGGAAGATGTTGCGATCCAAATGATCAAGTTGAAAGTGAAATATTACTTCCTGA
ACTCAAATGTGGTGATTGGCTTGTCTTAGAAGATTTTGGTGCATATCGAATCACAACAAG
TAGTAAATTCAATGGATTTCCTCAACACACCGTTTTCAATTATATTGAAAAAGAAATGTG
GGATTTTTTTATGAAAATAAAATTGTCTAATATTGAAGTTGGCTACCATATCAAGAAATA
A
>g15886.t3 Gene=g15886 Length=250
MSSTTLPKETVQIIDKFDLFQLVHDRIKEIGIDESFFITDVGDVVKKFILWKELFPRIEP
DFAIKSNNLPVIASTLAALGAGFDCASHGEITQVLEMGVEPEKIVFAQTVKPIYNIKLAK
EKNVFKMTFDNENELYKVKEHFPEAHLLLRLGFSPKSSNKIAFGAKFGCSFETGKDLLKK
AKELNLNVKGVAFHIGVGCEEYEIFRKAIEDSSKMFEYGKSLGFNMDVLDIGGGFPGHET
KTIVSFKSNQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g15886.t3 | Gene3D | G3DSA:3.20.20.10 | Alanine racemase | 42 | 249 | 8.7E-63 |
| 2 | g15886.t3 | PANTHER | PTHR11482 | ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE | 31 | 247 | 5.9E-76 |
| 3 | g15886.t3 | PANTHER | PTHR11482:SF6 | ORNITHINE DECARBOXYLASE 1-RELATED | 31 | 247 | 5.9E-76 |
| 5 | g15886.t3 | PRINTS | PR01182 | Ornithine decarboxylase signature | 34 | 58 | 5.3E-28 |
| 7 | g15886.t3 | PRINTS | PR01182 | Ornithine decarboxylase signature | 60 | 87 | 5.3E-28 |
| 10 | g15886.t3 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 62 | 80 | 3.3E-11 |
| 8 | g15886.t3 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 82 | 94 | 3.3E-11 |
| 6 | g15886.t3 | PRINTS | PR01182 | Ornithine decarboxylase signature | 104 | 128 | 5.3E-28 |
| 4 | g15886.t3 | PRINTS | PR01182 | Ornithine decarboxylase signature | 134 | 156 | 5.3E-28 |
| 9 | g15886.t3 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 185 | 198 | 3.3E-11 |
| 1 | g15886.t3 | Pfam | PF02784 | Pyridoxal-dependent decarboxylase, pyridoxal binding domain | 42 | 241 | 2.3E-57 |
| 12 | g15886.t3 | ProSitePatterns | PS00878 | Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. | 62 | 80 | - |
| 11 | g15886.t3 | SUPERFAMILY | SSF51419 | PLP-binding barrel | 36 | 238 | 6.38E-50 |
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