Gene loci information

Transcript annotation

  • This transcript has been annotated as Ornithine decarboxylase.

Parent gene

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.t7 TTS g4890.t7 5823116 5823116
chr_2 g4890 g4890.t7 isoform g4890.t7 5824055 5825202
chr_2 g4890 g4890.t7 exon g4890.t7.exon1 5824055 5824165
chr_2 g4890 g4890.t7 cds g4890.t7.CDS1 5824056 5824165
chr_2 g4890 g4890.t7 exon g4890.t7.exon2 5824223 5824482
chr_2 g4890 g4890.t7 cds g4890.t7.CDS2 5824223 5824482
chr_2 g4890 g4890.t7 exon g4890.t7.exon3 5824790 5825202
chr_2 g4890 g4890.t7 cds g4890.t7.CDS3 5824790 5825202
chr_2 g4890 g4890.t7 TSS g4890.t7 5825239 5825239

Sequences

>g4890.t7 Gene=g4890 Length=784
ATGAGTAAAGTTTTTAAATTTTTGTCCCACTTTCATTTAGAAAAATCAATTGAACGATCA
TTAAAAGTCGTGAATGATTCGCATTATATTTGCAATTTGAGTGATGTTATTCGAAAATAT
GAAGATTGGAAAACTCATTTGCCACGAGTGCGACCACATTATGCAGTAAAATGCAATGAC
AATATTAATGTTCTCAAAACTTTAGCATCTATTGGTTGCTCATTTGATTGTGCGTCAGCA
GGCGAGATTGAGAAAATTTTATCATTAAATGTCAATCCAGAACGAATTATTTTTGCAAAT
ACAACAAAATTTGCAAAGCATATCGAGTTTGCAGAACAAAATCAAGTGAACATCATGACG
TTTGATAATGAAGATGAACTTTATAAAATCCTTAAAATTCATCCAAGCGCAAATTTAGTT
TTGAGAATACGCTATAGCTCAGATAAGGCAATTTACAAATTGGGCAAAAAGTTTGGATCT
TTACCAAATACGGAAGCTCCTGAGTTGCTTAAATTAGCCAAAAGTTTAAATCTTAATGTC
ATTGGCATCAGTTTTCATATCGGTTCAAGCTGTGAAGATTATGAGGTTTATTGTGGAGCA
ATTGCAATTTCTAGAGTTTTATTTCAATTTGCTGCTGACATTGGCTATAACTTTAGAATC
CTTGATATCGGTGGTGGCTTTCCAGGAGATAATTTCAATCGAGTCAAAGAGTTTTCATGC
ATGATTAATAATGCATTGAATCAAAATTTTCCACTCAATGAATTTCCTAATCTGGAAATT
TTAT

>g4890.t7 Gene=g4890 Length=261
MSKVFKFLSHFHLEKSIERSLKVVNDSHYICNLSDVIRKYEDWKTHLPRVRPHYAVKCND
NINVLKTLASIGCSFDCASAGEIEKILSLNVNPERIIFANTTKFAKHIEFAEQNQVNIMT
FDNEDELYKILKIHPSANLVLRIRYSSDKAIYKLGKKFGSLPNTEAPELLKLAKSLNLNV
IGISFHIGSSCEDYEVYCGAIAISRVLFQFAADIGYNFRILDIGGGFPGDNFNRVKEFSC
MINNALNQNFPLNEFPNLEIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4890.t7 Gene3D G3DSA:3.20.20.10 Alanine racemase 34 261 6.0E-73
2 g4890.t7 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 23 253 4.5E-91
3 g4890.t7 PANTHER PTHR11482:SF6 ORNITHINE DECARBOXYLASE 1-RELATED 23 253 4.5E-91
4 g4890.t7 PRINTS PR01182 Ornithine decarboxylase signature 26 50 6.4E-34
7 g4890.t7 PRINTS PR01182 Ornithine decarboxylase signature 52 79 6.4E-34
8 g4890.t7 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 54 72 7.3E-16
10 g4890.t7 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 74 86 7.3E-16
5 g4890.t7 PRINTS PR01182 Ornithine decarboxylase signature 96 120 6.4E-34
6 g4890.t7 PRINTS PR01182 Ornithine decarboxylase signature 126 148 6.4E-34
9 g4890.t7 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 177 190 7.3E-16
1 g4890.t7 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 34 260 2.6E-66
12 g4890.t7 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. 54 72 -
11 g4890.t7 SUPERFAMILY SSF51419 PLP-binding barrel 28 259 4.8E-57

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