General information for g15886.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t4 | TTS | g15886.t4 | 7175648 | 7175648 |
| chr_4 | g15886 | g15886.t4 | isoform | g15886.t4 | 7175673 | 7177684 |
| chr_4 | g15886 | g15886.t4 | exon | g15886.t4.exon1 | 7175673 | 7176273 |
| chr_4 | g15886 | g15886.t4 | cds | g15886.t4.CDS1 | 7175797 | 7176273 |
| chr_4 | g15886 | g15886.t4 | exon | g15886.t4.exon2 | 7176333 | 7176382 |
| chr_4 | g15886 | g15886.t4 | cds | g15886.t4.CDS2 | 7176333 | 7176382 |
| chr_4 | g15886 | g15886.t4 | exon | g15886.t4.exon3 | 7176441 | 7176682 |
| chr_4 | g15886 | g15886.t4 | cds | g15886.t4.CDS3 | 7176441 | 7176682 |
| chr_4 | g15886 | g15886.t4 | exon | g15886.t4.exon4 | 7176742 | 7176899 |
| chr_4 | g15886 | g15886.t4 | cds | g15886.t4.CDS4 | 7176742 | 7176890 |
| chr_4 | g15886 | g15886.t4 | exon | g15886.t4.exon5 | 7177397 | 7177684 |
| chr_4 | g15886 | g15886.t4 | TSS | g15886.t4 | 7177702 | 7177702 |
Sequences
>g15886.t4 Gene=g15886 Length=1339
ATGTCGTCAACAACACTGCCTAAAGAAACTGTTCAAATTATTGATAAATTTGATTTATTT
CAATTAGTTCATGATCGGATTAAAGAGATTGGAATTGATGAATCATTTTTCATCACAGAC
GTTGGCGATGTTGTGAAGAAATTTATTTTATGGAAAGAATTATTTCCTCGTATTGAACCT
GATTTTGCAATTAAAAGTAATAATCTTCCTGTAATTGCTTCTACTTTGGCTGCTTTAGGT
AAACTTAAAGAAATTTTCTAATGTCTTATCTTGAAAGTTTTTCTGAAAGTTCTTGAAATG
GGTGTTGAACCAGAAAAAATTGTTTTTGCACAAACTGTTAAACCAATTTACAATATCAAA
TTGGCCAAAGAGAAGAATGTTTTTAAAATGACTTTTGATAATGAAAATGAACTTTATAAA
GTTAAGGAACATTTTCCAGAAGCTCATCTTCTTTTACGTCTTGGTTTTTCTCCAAAGTCA
TCAAATAAAATAGCTTTTGGTGCTAAATTTGGTTGTTCTTTTGAAACTGGCAAAGATTTA
TTGAAAAAGGCAAAAGAATTAAATTTAAATGTCAAAGGAGTTGCTTTTCATATTGGTGTC
GGTTGTGAAGAATATGAAATTTTTAGAAAGGCAATTGAAGACAGCAGCAAGATGTTTGAA
TATGGAAAATCTTTGGGTTTCAATATGGATGTTCTTGATATTGGAGGCGGATTTCCTGGC
CATGAAACTAAAACAATCCGTGAGGTTTCAAAAGTAATCAATGAAAGCATAGAACAAAAT
TTTCCCGATCCAAGTGTAAAAATAATTTCGGAGCCAGGCCAATTTTTTGCAACACATTCG
ATGACACTTGTGGTAAATGTTCATTCTAAAGCTGTAAAATTAAATGAAAATGGAGAAAAA
ATTTTCCATTATTACATCACGGATGGAATTTACCAATCATTTGCAATGAAAGGAAGTGGT
GGAAATAATCCGAATCCATTGGTTGTTAAAACACTTCGGGACACGAGTGGTGACAATTTA
AAGAAAAGTGTAATTTGGGGAAGATGTTGCGATCCAAATGATCAAGTTGAAAGTGAAATA
TTACTTCCTGAACTCAAATGTGGTGATTGGCTTGTCTTAGAAGATTTTGGTGCATATCGA
ATCACAACAAGTAGTAAATTCAATGGATTTCCTCAACACACCGTTTTCAATTATATTGAA
AAAGAAATGTGGTAAGATATAAAATTTTTTAAAAATTTAATTTTGATTTATTTTGACTAA
ATTAATATTTTACTTTAGGGATTTTTTTATGAAAATAAAATTGTCTAATATTGAAGTTGG
CTACCATATCAAGAAATAA
>g15886.t4 Gene=g15886 Length=305
MGVEPEKIVFAQTVKPIYNIKLAKEKNVFKMTFDNENELYKVKEHFPEAHLLLRLGFSPK
SSNKIAFGAKFGCSFETGKDLLKKAKELNLNVKGVAFHIGVGCEEYEIFRKAIEDSSKMF
EYGKSLGFNMDVLDIGGGFPGHETKTIREVSKVINESIEQNFPDPSVKIISEPGQFFATH
SMTLVVNVHSKAVKLNENGEKIFHYYITDGIYQSFAMKGSGGNNPNPLVVKTLRDTSGDN
LKKSVIWGRCCDPNDQVESEILLPELKCGDWLVLEDFGAYRITTSSKFNGFPQHTVFNYI
EKEMW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g15886.t4 | Gene3D | G3DSA:3.20.20.10 | Alanine racemase | 1 | 177 | 0 |
| 14 | g15886.t4 | Gene3D | G3DSA:2.40.37.10 | Lyase | 178 | 300 | 0 |
| 3 | g15886.t4 | PANTHER | PTHR11482 | ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE | 1 | 303 | 0 |
| 7 | g15886.t4 | PRINTS | PR01182 | Ornithine decarboxylase signature | 8 | 32 | 0 |
| 5 | g15886.t4 | PRINTS | PR01182 | Ornithine decarboxylase signature | 38 | 60 | 0 |
| 8 | g15886.t4 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 89 | 102 | 0 |
| 9 | g15886.t4 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 169 | 188 | 0 |
| 6 | g15886.t4 | PRINTS | PR01182 | Ornithine decarboxylase signature | 245 | 255 | 0 |
| 4 | g15886.t4 | PRINTS | PR01182 | Ornithine decarboxylase signature | 265 | 278 | 0 |
| 10 | g15886.t4 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 278 | 291 | 0 |
| 1 | g15886.t4 | Pfam | PF02784 | Pyridoxal-dependent decarboxylase, pyridoxal binding domain | 1 | 178 | 0 |
| 2 | g15886.t4 | Pfam | PF00278 | Pyridoxal-dependent decarboxylase, C-terminal sheet domain | 180 | 278 | 0 |
| 11 | g15886.t4 | SUPERFAMILY | SSF51419 | PLP-binding barrel | 1 | 180 | 0 |
| 12 | g15886.t4 | SUPERFAMILY | SSF50621 | Alanine racemase C-terminal domain-like | 160 | 303 | 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