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 g7186 g7186.t1 TTS g7186.t1 21971182 21971182
chr_2 g7186 g7186.t1 isoform g7186.t1 21971673 21972830
chr_2 g7186 g7186.t1 exon g7186.t1.exon1 21971673 21972830
chr_2 g7186 g7186.t1 cds g7186.t1.CDS1 21971673 21972830
chr_2 g7186 g7186.t1 TSS g7186.t1 NA NA

Sequences

>g7186.t1 Gene=g7186 Length=1158
ATGGAATTATTTAGTAGTGAGATCGAGAGTCGTTTACATTCAAATAATGATAATCCGTTC
TTTATTTTGAATGTCAATGATATCCGTACAAAGATAAAAAAATGGAAGCAAACGATTCCA
CGGGCTATTCCATATTATGCTGTCAAGTGCAATGATAACGAATTAGTTCTCAAAGTTCTT
GCGGAAAATGGAACTGGATTTGATTGTGCTTCTAAAAATGAAATTTCAAAAGTTTTGAAG
TTAGGAGTTGACTGTGAAAAAATTATTTACTCAAACACCGTAAAGCAAATTTCACATTTG
AAATATGCGGCAAAAATGATGGTTCAAAAGGTTACATTTGATTCGGTTGAAGAATTGGAA
AAAATAAAAGCATTTCATCCAAATGCTCAAGTTGTATTGAGAATTCGTTTCGATTCAAAC
AATTCTATCGTAAATCTTGGTACAAAATTTGGCTGCGATCCAGTTAAAACTGCTCCTAAG
TTAATTGAACTATGTCAAAAGATGAATATGAATTTGATTGGATTACATTTCCATGTTGGA
TCGTGGAATCGAAACTATGAAATTTTCACACAAGCTTTAGCTACTATTCGAAAGCTTTTC
AATTTTGCTGAGACATGTAGTATTAAATTAAACTTTATTGATATTGGTGGCGGTTTCATT
GGAGAAGATTTGTTACTACTTGACCTCTATGCAAAATCAATTAATGCAGGAATAAATGAC
AATTTTCCAAGCGACAAAATCAAAATAATTTCAGAACCCGGCCGATTTTTTGTTGATTCA
GCGTTCAAACTCGTCACCCAAATCATTTTGAAAAAACTCGACGAAGAGGATGGGCGAATT
CATTATTATCTAAACGAGAGCATTTACATGTCATTTATGGCAACCTTTCTCTACAACCTG
AAGCCATTAACTTCCGTGATCAAGAGATCAAAGGGTAAAAATGATTTTGCTGAGGAAAAA
TTGTCGACAATTTGGGGCTGCTCATGCAATTCAAATGACAAAATTGTGGATAATGTGATG
CTAAGAGAAATGGAAATGGGTGATTGGCTCGTGTTTCATAACATGGGAGCTTATACTTTA
TCAGTTTCAACAAAATTCAATGGATTTCAAAATAATGAGGTTTTGGTTATTGATGAGGAA
AGACAAACTGAATACTGA

>g7186.t1 Gene=g7186 Length=385
MELFSSEIESRLHSNNDNPFFILNVNDIRTKIKKWKQTIPRAIPYYAVKCNDNELVLKVL
AENGTGFDCASKNEISKVLKLGVDCEKIIYSNTVKQISHLKYAAKMMVQKVTFDSVEELE
KIKAFHPNAQVVLRIRFDSNNSIVNLGTKFGCDPVKTAPKLIELCQKMNMNLIGLHFHVG
SWNRNYEIFTQALATIRKLFNFAETCSIKLNFIDIGGGFIGEDLLLLDLYAKSINAGIND
NFPSDKIKIISEPGRFFVDSAFKLVTQIILKKLDEEDGRIHYYLNESIYMSFMATFLYNL
KPLTSVIKRSKGKNDFAEEKLSTIWGCSCNSNDKIVDNVMLREMEMGDWLVFHNMGAYTL
SVSTKFNGFQNNEVLVIDEERQTEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g7186.t1 CDD cd00622 PLPDE_III_ODC 17 377 7.76429E-153
19 g7186.t1 Gene3D G3DSA:2.40.37.10 Lyase 6 370 4.2E-123
18 g7186.t1 Gene3D G3DSA:3.20.20.10 Alanine racemase 26 257 4.2E-123
3 g7186.t1 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 9 377 3.1E-125
8 g7186.t1 PRINTS PR01182 Ornithine decarboxylase signature 18 42 3.4E-44
4 g7186.t1 PRINTS PR01182 Ornithine decarboxylase signature 44 71 3.4E-44
13 g7186.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 46 64 3.9E-32
11 g7186.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 66 78 3.9E-32
6 g7186.t1 PRINTS PR01182 Ornithine decarboxylase signature 88 112 3.4E-44
9 g7186.t1 PRINTS PR01182 Ornithine decarboxylase signature 118 140 3.4E-44
10 g7186.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 169 182 3.9E-32
12 g7186.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 249 268 3.9E-32
5 g7186.t1 PRINTS PR01182 Ornithine decarboxylase signature 323 333 3.4E-44
7 g7186.t1 PRINTS PR01182 Ornithine decarboxylase signature 343 356 3.4E-44
14 g7186.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 356 369 3.9E-32
1 g7186.t1 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 26 258 1.6E-69
2 g7186.t1 Pfam PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain 259 356 2.4E-14
17 g7186.t1 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. 46 64 -
15 g7186.t1 SUPERFAMILY SSF51419 PLP-binding barrel 17 261 1.74E-61
16 g7186.t1 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like 233 376 9.84E-31

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