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 g15886 g15886.t1 TTS g15886.t1 7175648 7175648
chr_4 g15886 g15886.t1 isoform g15886.t1 7175673 7177684
chr_4 g15886 g15886.t1 exon g15886.t1.exon1 7175673 7175733
chr_4 g15886 g15886.t1 cds g15886.t1.CDS1 7175673 7175733
chr_4 g15886 g15886.t1 exon g15886.t1.exon2 7175801 7176273
chr_4 g15886 g15886.t1 cds g15886.t1.CDS2 7175801 7176273
chr_4 g15886 g15886.t1 exon g15886.t1.exon3 7176333 7176382
chr_4 g15886 g15886.t1 cds g15886.t1.CDS3 7176333 7176382
chr_4 g15886 g15886.t1 exon g15886.t1.exon4 7176441 7176682
chr_4 g15886 g15886.t1 cds g15886.t1.CDS4 7176441 7176682
chr_4 g15886 g15886.t1 exon g15886.t1.exon5 7176742 7176899
chr_4 g15886 g15886.t1 cds g15886.t1.CDS5 7176742 7176899
chr_4 g15886 g15886.t1 exon g15886.t1.exon6 7177184 7177224
chr_4 g15886 g15886.t1 cds g15886.t1.CDS6 7177184 7177224
chr_4 g15886 g15886.t1 exon g15886.t1.exon7 7177447 7177684
chr_4 g15886 g15886.t1 cds g15886.t1.CDS7 7177447 7177684
chr_4 g15886 g15886.t1 TSS g15886.t1 7177702 7177702

Sequences

>g15886.t1 Gene=g15886 Length=1263
ATGTCGTCAACAACACTGCCTAAAGAAACTGTTCAAATTATTGATAAATTTGATTTATTT
CAATTAGTTCATGATCGGATTAAAGAGATTGGAATTGATGAATCATTTTTCATCACAGAC
GTTGGCGATGTTGTGAAGAAATTTATTTTATGGAAAGAATTATTTCCTCGTATTGAACCT
GATTTTGCAATTAAAAGTAATAATCTTCCTGTAATTGCTTCTACTTTGGCTGCTTTAGGT
GCTGGTTTTGATTGTGCAAGTCATGGAGAGATAACACAAGTTCTTGAAATGGGTGTTGAA
CCAGAAAAAATTGTTTTTGCACAAACTGTTAAACCAATTTACAATATCAAATTGGCCAAA
GAGAAGAATGTTTTTAAAATGACTTTTGATAATGAAAATGAACTTTATAAAGTTAAGGAA
CATTTTCCAGAAGCTCATCTTCTTTTACGTCTTGGTTTTTCTCCAAAGTCATCAAATAAA
ATAGCTTTTGGTGCTAAATTTGGTTGTTCTTTTGAAACTGGCAAAGATTTATTGAAAAAG
GCAAAAGAATTAAATTTAAATGTCAAAGGAGTTGCTTTTCATATTGGTGTCGGTTGTGAA
GAATATGAAATTTTTAGAAAGGCAATTGAAGACAGCAGCAAGATGTTTGAATATGGAAAA
TCTTTGGGTTTCAATATGGATGTTCTTGATATTGGAGGCGGATTTCCTGGCCATGAAACT
AAAACAATCCGTGAGGTTTCAAAAGTAATCAATGAAAGCATAGAACAAAATTTTCCCGAT
CCAAGTGTAAAAATAATTTCGGAGCCAGGCCAATTTTTTGCAACACATTCGATGACACTT
GTGGTAAATGTTCATTCTAAAGCTGTAAAATTAAATGAAAATGGAGAAAAAATTTTCCAT
TATTACATCACGGATGGAATTTACCAATCATTTGCAATGAAAGGAAGTGGTGGAAATAAT
CCGAATCCATTGGTTGTTAAAACACTTCGGGACACGAGTGGTGACAATTTAAAGAAAAGT
GTAATTTGGGGAAGATGTTGCGATCCAAATGATCAAGTTGAAAGTGAAATATTACTTCCT
GAACTCAAATGTGGTGATTGGCTTGTCTTAGAAGATTTTGGTGCATATCGAATCACAACA
AGTAGTAAATTCAATGGATTTCCTCAACACACCGTTTTCAATTATATTGAAAAAGAAATG
TGGGATTTTTTTATGAAAATAAAATTGTCTAATATTGAAGTTGGCTACCATATCAAGAAA
TAA

>g15886.t1 Gene=g15886 Length=420
MSSTTLPKETVQIIDKFDLFQLVHDRIKEIGIDESFFITDVGDVVKKFILWKELFPRIEP
DFAIKSNNLPVIASTLAALGAGFDCASHGEITQVLEMGVEPEKIVFAQTVKPIYNIKLAK
EKNVFKMTFDNENELYKVKEHFPEAHLLLRLGFSPKSSNKIAFGAKFGCSFETGKDLLKK
AKELNLNVKGVAFHIGVGCEEYEIFRKAIEDSSKMFEYGKSLGFNMDVLDIGGGFPGHET
KTIREVSKVINESIEQNFPDPSVKIISEPGQFFATHSMTLVVNVHSKAVKLNENGEKIFH
YYITDGIYQSFAMKGSGGNNPNPLVVKTLRDTSGDNLKKSVIWGRCCDPNDQVESEILLP
ELKCGDWLVLEDFGAYRITTSSKFNGFPQHTVFNYIEKEMWDFFMKIKLSNIEVGYHIKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g15886.t1 CDD cd00622 PLPDE_III_ODC 33 393 4.97974E-149
20 g15886.t1 Gene3D G3DSA:2.40.37.10 Lyase 30 396 1.6E-124
19 g15886.t1 Gene3D G3DSA:3.20.20.10 Alanine racemase 44 273 1.6E-124
3 g15886.t1 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 31 402 8.2E-123
4 g15886.t1 PANTHER PTHR11482:SF6 ORNITHINE DECARBOXYLASE 1-RELATED 31 402 8.2E-123
8 g15886.t1 PRINTS PR01182 Ornithine decarboxylase signature 34 58 6.9E-35
10 g15886.t1 PRINTS PR01182 Ornithine decarboxylase signature 60 87 6.9E-35
15 g15886.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 62 80 4.2E-25
13 g15886.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 82 94 4.2E-25
9 g15886.t1 PRINTS PR01182 Ornithine decarboxylase signature 104 128 6.9E-35
7 g15886.t1 PRINTS PR01182 Ornithine decarboxylase signature 134 156 6.9E-35
14 g15886.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 185 198 4.2E-25
11 g15886.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 265 284 4.2E-25
6 g15886.t1 PRINTS PR01182 Ornithine decarboxylase signature 341 351 6.9E-35
5 g15886.t1 PRINTS PR01182 Ornithine decarboxylase signature 361 374 6.9E-35
12 g15886.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 374 387 4.2E-25
1 g15886.t1 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 42 274 2.4E-65
2 g15886.t1 Pfam PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain 275 374 6.8E-13
18 g15886.t1 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. 62 80 -
16 g15886.t1 SUPERFAMILY SSF51419 PLP-binding barrel 36 276 1.05E-54
17 g15886.t1 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like 256 401 3.98E-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