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_4 g16333 g16333.t1 isoform g16333.t1 9108117 9109851
chr_4 g16333 g16333.t1 exon g16333.t1.exon1 9108117 9108168
chr_4 g16333 g16333.t1 cds g16333.t1.CDS1 9108117 9108168
chr_4 g16333 g16333.t1 exon g16333.t1.exon2 9108267 9108656
chr_4 g16333 g16333.t1 cds g16333.t1.CDS2 9108267 9108656
chr_4 g16333 g16333.t1 exon g16333.t1.exon3 9108709 9108832
chr_4 g16333 g16333.t1 cds g16333.t1.CDS3 9108709 9108832
chr_4 g16333 g16333.t1 exon g16333.t1.exon4 9108887 9109146
chr_4 g16333 g16333.t1 cds g16333.t1.CDS4 9108887 9109146
chr_4 g16333 g16333.t1 exon g16333.t1.exon5 9109439 9109851
chr_4 g16333 g16333.t1 cds g16333.t1.CDS5 9109439 9109851
chr_4 g16333 g16333.t1 TSS g16333.t1 NA NA
chr_4 g16333 g16333.t1 TTS g16333.t1 NA NA

Sequences

>g16333.t1 Gene=g16333 Length=1239
ATGAGTAAAATTTTTTATTATTTTTCTCACTTTCATTTAGAAAAATCCATTGAAAGATCA
TTGAAAGTTGAGAATGATTCGCATTATATTTGCAATTTGAGTGATCTTATTCGAAAATAT
GAAGATTGGAAAACTTATTTGCCACGAGTTAAACCATATTATGCAGTAAAATGCAATGAC
AATATTAACGTTCTCAAACTATTAGCATTTATTGGTTGCTCATTTGATTGTGCATCAGCA
GGCGAGATTGAGAAAATTTTATCATTAAACGTCGGTCCAGAACGAATTATTTTTGCAAAT
ACAACGAAATTTGCAAAGCATATCGAATTTGCAGAACGTCATAAAGTAAACCTCATGACA
TTTGATAATGAAGATGAACTTTATAAAATTTTGAAGATTTATCCAAACGCAAAATTAATC
TTGAGAATACGCTATGGCTCAGATAAGGCACTTTACAAATTGAGCGAAAAATTTGGATCT
TTACCAAATACGGAAGCACCTGAGCTGCTTAAATTAGCAAAAAGGTTAAAACTTAATGTT
GTTGGCATCAGTTTTCATATTGGTTCACGTTGTGAAGATTATAAAGTTTATTGCAGAGCA
ATTGCGATTTCCAGAGCTTTGTTTCAATTTGCTGCTGACATTGGCTTTAAGTTTAAAATT
CTTGATATTGGTGGTGGCTTTCCAGGAGATAATTTTAATCGAATCAAAGAATTTTCTATC
ATAATTAATGATGCATTGAATCGAAATTTTCCACTTGATGAGTTTCCTAATCTAGAAATT
GTATCTGAACCAGGAAGGTATTTTGTTGAATCTGCTTTTACTCTTGTCACTCAAATTCAC
TCACGAAAAATCACAAGAGATGCTAATGGGAAAATTGTTAGTGTCATGTATTATCTGAAC
GAAGGAATTTATTCAAATTTCCTTTTCATACCACTTGGACCTGAAAAAGTGACACCGAAA
ATTCTTTCACATAAACGTACGAATGAAAAATTTAAAACAACACTTTGGGGTCCAACACTT
GATTCAATTGACAAAATCTGTCAAAACATTGAATTAGAATTGCTTGAAATTGATGATGTT
ATTTATTTTATTAATATGGGAGCATACACAACTACTGTGGGCACAAACTTCAATAGTTTT
TCAGCAAAAACAAACATTGTTTACTTCCTGGAAAAAAATATTGAAAGCAACAAATTAAAC
ACTGAACTATTTGATTTTAACTTCATCAACGACACATGA

>g16333.t1 Gene=g16333 Length=412
MSKIFYYFSHFHLEKSIERSLKVENDSHYICNLSDLIRKYEDWKTYLPRVKPYYAVKCND
NINVLKLLAFIGCSFDCASAGEIEKILSLNVGPERIIFANTTKFAKHIEFAERHKVNLMT
FDNEDELYKILKIYPNAKLILRIRYGSDKALYKLSEKFGSLPNTEAPELLKLAKRLKLNV
VGISFHIGSRCEDYKVYCRAIAISRALFQFAADIGFKFKILDIGGGFPGDNFNRIKEFSI
IINDALNRNFPLDEFPNLEIVSEPGRYFVESAFTLVTQIHSRKITRDANGKIVSVMYYLN
EGIYSNFLFIPLGPEKVTPKILSHKRTNEKFKTTLWGPTLDSIDKICQNIELELLEIDDV
IYFINMGAYTTTVGTNFNSFSAKTNIVYFLEKNIESNKLNTELFDFNFINDT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g16333.t1 CDD cd00622 PLPDE_III_ODC 29 389 1.51958E-150
20 g16333.t1 Gene3D G3DSA:2.40.37.10 Lyase 17 381 1.3E-129
19 g16333.t1 Gene3D G3DSA:3.20.20.10 Alanine racemase 34 268 1.3E-129
3 g16333.t1 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 22 396 2.0E-132
4 g16333.t1 PANTHER PTHR11482:SF6 ORNITHINE DECARBOXYLASE 1-RELATED 22 396 2.0E-132
5 g16333.t1 PRINTS PR01182 Ornithine decarboxylase signature 26 50 4.9E-39
10 g16333.t1 PRINTS PR01182 Ornithine decarboxylase signature 52 79 4.9E-39
12 g16333.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 54 72 3.6E-31
15 g16333.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 74 86 3.6E-31
6 g16333.t1 PRINTS PR01182 Ornithine decarboxylase signature 96 120 4.9E-39
7 g16333.t1 PRINTS PR01182 Ornithine decarboxylase signature 126 148 4.9E-39
14 g16333.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 177 190 3.6E-31
11 g16333.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 260 279 3.6E-31
9 g16333.t1 PRINTS PR01182 Ornithine decarboxylase signature 334 344 4.9E-39
8 g16333.t1 PRINTS PR01182 Ornithine decarboxylase signature 354 367 4.9E-39
13 g16333.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 367 380 3.6E-31
1 g16333.t1 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 34 269 4.5E-70
2 g16333.t1 Pfam PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain 270 367 1.8E-13
18 g16333.t1 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. 54 72 -
16 g16333.t1 SUPERFAMILY SSF51419 PLP-binding barrel 28 272 1.24E-61
17 g16333.t1 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like 253 383 7.74E-27

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