Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ornithine decarboxylase 1.

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.t4 TTS g4890.t4 5823116 5823116
chr_2 g4890 g4890.t4 isoform g4890.t4 5823450 5824166
chr_2 g4890 g4890.t4 exon g4890.t4.exon1 5823450 5823977
chr_2 g4890 g4890.t4 cds g4890.t4.CDS1 5823584 5823977
chr_2 g4890 g4890.t4 exon g4890.t4.exon2 5824042 5824166
chr_2 g4890 g4890.t4 cds g4890.t4.CDS2 5824042 5824118
chr_2 g4890 g4890.t4 TSS g4890.t4 NA NA

Sequences

>g4890.t4 Gene=g4890 Length=653
GGTGGCTTTCCAGGAGATAATTTCAATCGAGTCAAAGAGTTTTCATGCATGATTAATAAT
GCATTGAATCAAAATTTTCCACTCAATGAATTTCCTAATCTGGAAATTTTATCTGAACCG
GGAAGATATTTCGTTGAATCTGCTTTTACTCTCGTCACTCAAATTCATTCACGAAAAATC
ACAAGAGATGCAGATGGGAAAATTGTTGATGTGATGTATTATCTAAATGAAGGAGTTTAC
TCAAATTTCCTTTTCATACCACTCGGTCCTGAAGAAGTAATACCAAAAATTCTTTCACAT
AAACGTACGAATGAGCAATTTAGAAGCACGATTTGGGGTCCGACATGCGATTCAACTGAC
AAAATTTGTGAGGACATTAAATTAGAATTGCTAGAAATTGGTGATGTTATTTATTTCACT
AATATGGGAGCTTACACAATTCCTTTGAGTACAAGCTTCAATGGTTTCCCAACAACAAAA
ATTGTTTACTTCTTGGAAGAGAATGTCGTTGATAGGTGAGGGAAAAAACTAAAAATAATT
TATCAAATTATTCCGAAATAATTTGTAATACATTAAATTAATTAATTAATTACATTTGCA
GCAACAAATTAAACACTGAAATGTTTGATTTTAACTTCATCAACGACGCATGA

>g4890.t4 Gene=g4890 Length=156
MINNALNQNFPLNEFPNLEILSEPGRYFVESAFTLVTQIHSRKITRDADGKIVDVMYYLN
EGVYSNFLFIPLGPEEVIPKILSHKRTNEQFRSTIWGPTCDSTDKICEDIKLELLEIGDV
IYFTNMGAYTIPLSTSFNGFPTTKIVYFLEENVVDR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4890.t4 Gene3D G3DSA:2.40.37.10 Lyase 1 156 0.0e+00
2 g4890.t4 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 2 151 0.0e+00
3 g4890.t4 PANTHER PTHR11482:SF6 ORNITHINE DECARBOXYLASE 1-RELATED 2 151 0.0e+00
7 g4890.t4 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 20 39 0.0e+00
4 g4890.t4 PRINTS PR01182 Ornithine decarboxylase signature 61 74 2.5e-05
6 g4890.t4 PRINTS PR01182 Ornithine decarboxylase signature 94 104 2.5e-05
5 g4890.t4 PRINTS PR01182 Ornithine decarboxylase signature 114 127 2.5e-05
8 g4890.t4 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 127 140 0.0e+00
1 g4890.t4 Pfam PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain 27 127 0.0e+00
9 g4890.t4 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like 8 152 0.0e+00

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