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_1 g13026 g13026.t1 TSS g13026.t1 27585941 27585941
chr_1 g13026 g13026.t1 isoform g13026.t1 27585967 27587100
chr_1 g13026 g13026.t1 exon g13026.t1.exon1 27585967 27587100
chr_1 g13026 g13026.t1 cds g13026.t1.CDS1 27585967 27587100
chr_1 g13026 g13026.t1 TTS g13026.t1 27587182 27587182

Sequences

>g13026.t1 Gene=g13026 Length=1134
ATGGATTTAATTAAATTAATTGAAAGTCGTTTAGCAGAAGGCAATGATGATTCATTTTAT
ATTCTTAATCTTGAGGATGTACGTTTGAAATACCGTTTATGGATGGAAAAAATTCCACGA
GTTGTGCCTTATTATGCTGTAAAGTGTAACGATCTTGAGGAAGTGCTAAATACTTTGAGA
GATTTGGGTGCAGGTTTTGACTGTGCTTCAAAGAAAGAAATTCATCAAATGCTTGCATTA
AACGTTGATAAGGAAAAAATTTTGTATACACACACTGCAAAGCAAATTTCACATCTGAAA
TATTCAGCTGAACAAAATATTGAGAAAATTACATTTGACTCTGTGGAAGAATTAGAAAAG
ATAAAAAAAGTTCATCCAAATGCGAAAGTTGTTTTAAGAATTCGATTTGATGCAGCTTCT
TCTATCATTAATTTGGGAATTAAATTCGGATGTGACCCGATAAAAGAAGCACCAAAATTC
ATTGAACTTTGTAAAGATATGAATATGAATTTGATTGGTATATCTTTTCATGTGGGATCA
GGAACTCAGGATTTTGGTATTTTTGAAAGAGCTTTAGCAACTGTTCGTGAACTTTTCGAT
TTTGCTGCAACAATTGGTTTCAAACTGAATTTCGTGGATATCGGTGGTGGATTTATTGGA
GAAAACATTTCTTTACTCGATAATTATGCAAAATCAATAAATACAGGCATTGATAAAAAT
TTCCCTTCAAGCAATGAAGTTGAAATTGTTGCTGAGCCAGGAAGATATTTCGTTGATTCA
GCATTTTCAATTGCTACACAAATTGTTTTGAAAAAATCTGGAACTGATGGTCAAATTCAT
TACTACCTCAACGAAAGCATTTACATGTCATTTCTCATTGCGTTTCTTTATAAATCTGAT
TTGAAATTTACAATAATCAGAAAATCAAAAATGGAAAATGAAACAAAAAGTGAAAAGTTG
TCAACACTTTGGGGATGCACGTGCAATTCAATGGATAAAATAATGGGTGACTGCATGATG
AAAGAAATGGAAATTGGAGATTGGTTGATTTTTCATAATATGGGTGCATATACATTGACT
GTCTCAACTAAATTCAATGGATTTGAAAATAATAAAGTTTTTATTTTAAAGTAA

>g13026.t1 Gene=g13026 Length=377
MDLIKLIESRLAEGNDDSFYILNLEDVRLKYRLWMEKIPRVVPYYAVKCNDLEEVLNTLR
DLGAGFDCASKKEIHQMLALNVDKEKILYTHTAKQISHLKYSAEQNIEKITFDSVEELEK
IKKVHPNAKVVLRIRFDAASSIINLGIKFGCDPIKEAPKFIELCKDMNMNLIGISFHVGS
GTQDFGIFERALATVRELFDFAATIGFKLNFVDIGGGFIGENISLLDNYAKSINTGIDKN
FPSSNEVEIVAEPGRYFVDSAFSIATQIVLKKSGTDGQIHYYLNESIYMSFLIAFLYKSD
LKFTIIRKSKMENETKSEKLSTLWGCTCNSMDKIMGDCMMKEMEIGDWLIFHNMGAYTLT
VSTKFNGFENNKVFILK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g13026.t1 CDD cd00622 PLPDE_III_ODC 16 376 7.45449E-161
19 g13026.t1 Gene3D G3DSA:2.40.37.10 Lyase 14 375 9.1E-127
18 g13026.t1 Gene3D G3DSA:3.20.20.10 Alanine racemase 27 257 9.1E-127
3 g13026.t1 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 7 375 1.2E-128
4 g13026.t1 PANTHER PTHR11482:SF6 ORNITHINE DECARBOXYLASE 1-RELATED 7 375 1.2E-128
7 g13026.t1 PRINTS PR01182 Ornithine decarboxylase signature 17 41 4.3E-44
5 g13026.t1 PRINTS PR01182 Ornithine decarboxylase signature 43 70 4.3E-44
14 g13026.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 45 63 2.7E-30
11 g13026.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 65 77 2.7E-30
10 g13026.t1 PRINTS PR01182 Ornithine decarboxylase signature 87 111 4.3E-44
6 g13026.t1 PRINTS PR01182 Ornithine decarboxylase signature 117 139 4.3E-44
15 g13026.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 168 181 2.7E-30
12 g13026.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 249 268 2.7E-30
8 g13026.t1 PRINTS PR01182 Ornithine decarboxylase signature 322 332 4.3E-44
9 g13026.t1 PRINTS PR01182 Ornithine decarboxylase signature 342 355 4.3E-44
13 g13026.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 355 368 2.7E-30
1 g13026.t1 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 25 258 2.2E-68
2 g13026.t1 Pfam PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain 259 355 2.0E-15
21 g13026.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 278 -
22 g13026.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 279 297 -
20 g13026.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 298 377 -
24 g13026.t1 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. 45 63 -
16 g13026.t1 SUPERFAMILY SSF51419 PLP-binding barrel 18 261 8.67E-60
17 g13026.t1 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like 238 374 1.21E-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

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.

Raw TPM values