Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t1 TTS g4890.t1 5823116 5823116
chr_2 g4890 g4890.t1 isoform g4890.t1 5823450 5825202
chr_2 g4890 g4890.t1 exon g4890.t1.exon1 5823450 5823501
chr_2 g4890 g4890.t1 cds g4890.t1.CDS1 5823450 5823501
chr_2 g4890 g4890.t1 exon g4890.t1.exon2 5823588 5823977
chr_2 g4890 g4890.t1 cds g4890.t1.CDS2 5823588 5823977
chr_2 g4890 g4890.t1 exon g4890.t1.exon3 5824042 5824165
chr_2 g4890 g4890.t1 cds g4890.t1.CDS3 5824042 5824165
chr_2 g4890 g4890.t1 exon g4890.t1.exon4 5824223 5824482
chr_2 g4890 g4890.t1 cds g4890.t1.CDS4 5824223 5824482
chr_2 g4890 g4890.t1 exon g4890.t1.exon5 5824790 5825202
chr_2 g4890 g4890.t1 cds g4890.t1.CDS5 5824790 5825202
chr_2 g4890 g4890.t1 TSS g4890.t1 5825239 5825239

Sequences

>g4890.t1 Gene=g4890 Length=1239
ATGAGTAAAGTTTTTAAATTTTTGTCCCACTTTCATTTAGAAAAATCAATTGAACGATCA
TTAAAAGTCGTGAATGATTCGCATTATATTTGCAATTTGAGTGATGTTATTCGAAAATAT
GAAGATTGGAAAACTCATTTGCCACGAGTGCGACCACATTATGCAGTAAAATGCAATGAC
AATATTAATGTTCTCAAAACTTTAGCATCTATTGGTTGCTCATTTGATTGTGCGTCAGCA
GGCGAGATTGAGAAAATTTTATCATTAAATGTCAATCCAGAACGAATTATTTTTGCAAAT
ACAACAAAATTTGCAAAGCATATCGAGTTTGCAGAACAAAATCAAGTGAACATCATGACG
TTTGATAATGAAGATGAACTTTATAAAATCCTTAAAATTCATCCAAGCGCAAATTTAGTT
TTGAGAATACGCTATAGCTCAGATAAGGCAATTTACAAATTGGGCAAAAAGTTTGGATCT
TTACCAAATACGGAAGCTCCTGAGTTGCTTAAATTAGCCAAAAGTTTAAATCTTAATGTC
ATTGGCATCAGTTTTCATATCGGTTCAAGCTGTGAAGATTATGAGGTTTATTGTGGAGCA
ATTGCAATTTCTAGAGTTTTATTTCAATTTGCTGCTGACATTGGCTATAACTTTAGAATC
CTTGATATCGGTGGTGGCTTTCCAGGAGATAATTTCAATCGAGTCAAAGAGTTTTCATGC
ATGATTAATAATGCATTGAATCAAAATTTTCCACTCAATGAATTTCCTAATCTGGAAATT
TTATCTGAACCGGGAAGATATTTCGTTGAATCTGCTTTTACTCTCGTCACTCAAATTCAT
TCACGAAAAATCACAAGAGATGCAGATGGGAAAATTGTTGATGTGATGTATTATCTAAAT
GAAGGAGTTTACTCAAATTTCCTTTTCATACCACTCGGTCCTGAAGAAGTAATACCAAAA
ATTCTTTCACATAAACGTACGAATGAGCAATTTAGAAGCACGATTTGGGGTCCGACATGC
GATTCAACTGACAAAATTTGTGAGGACATTAAATTAGAATTGCTAGAAATTGGTGATGTT
ATTTATTTCACTAATATGGGAGCTTACACAATTCCTTTGAGTACAAGCTTCAATGGTTTC
CCAACAACAAAAATTGTTTACTTCTTGGAAGAGAATGTCGTTGATAGCAACAAATTAAAC
ACTGAAATGTTTGATTTTAACTTCATCAACGACGCATGA

>g4890.t1 Gene=g4890 Length=412
MSKVFKFLSHFHLEKSIERSLKVVNDSHYICNLSDVIRKYEDWKTHLPRVRPHYAVKCND
NINVLKTLASIGCSFDCASAGEIEKILSLNVNPERIIFANTTKFAKHIEFAEQNQVNIMT
FDNEDELYKILKIHPSANLVLRIRYSSDKAIYKLGKKFGSLPNTEAPELLKLAKSLNLNV
IGISFHIGSSCEDYEVYCGAIAISRVLFQFAADIGYNFRILDIGGGFPGDNFNRVKEFSC
MINNALNQNFPLNEFPNLEILSEPGRYFVESAFTLVTQIHSRKITRDADGKIVDVMYYLN
EGVYSNFLFIPLGPEEVIPKILSHKRTNEQFRSTIWGPTCDSTDKICEDIKLELLEIGDV
IYFTNMGAYTIPLSTSFNGFPTTKIVYFLEENVVDSNKLNTEMFDFNFINDA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g4890.t1 CDD cd00622 PLPDE_III_ODC 29 388 8.03684E-173
20 g4890.t1 Gene3D G3DSA:2.40.37.10 Lyase 25 389 2.9E-134
19 g4890.t1 Gene3D G3DSA:3.20.20.10 Alanine racemase 36 268 2.9E-134
3 g4890.t1 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 23 392 3.4E-137
4 g4890.t1 PANTHER PTHR11482:SF6 ORNITHINE DECARBOXYLASE 1-RELATED 23 392 3.4E-137
5 g4890.t1 PRINTS PR01182 Ornithine decarboxylase signature 26 50 1.3E-42
10 g4890.t1 PRINTS PR01182 Ornithine decarboxylase signature 52 79 1.3E-42
12 g4890.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 54 72 3.1E-32
15 g4890.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 74 86 3.1E-32
6 g4890.t1 PRINTS PR01182 Ornithine decarboxylase signature 96 120 1.3E-42
7 g4890.t1 PRINTS PR01182 Ornithine decarboxylase signature 126 148 1.3E-42
14 g4890.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 177 190 3.1E-32
11 g4890.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 260 279 3.1E-32
9 g4890.t1 PRINTS PR01182 Ornithine decarboxylase signature 334 344 1.3E-42
8 g4890.t1 PRINTS PR01182 Ornithine decarboxylase signature 354 367 1.3E-42
13 g4890.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 367 380 3.1E-32
1 g4890.t1 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 34 269 1.3E-71
2 g4890.t1 Pfam PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain 270 367 9.7E-17
18 g4890.t1 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. 54 72 -
16 g4890.t1 SUPERFAMILY SSF51419 PLP-binding barrel 28 272 2.62E-62
17 g4890.t1 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like 246 392 9.63E-33

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

Pathway

  • This transcript belongs to the following pathways

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