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_1 g13027 g13027.t1 TSS g13027.t1 27587215 27587215
chr_1 g13027 g13027.t1 isoform g13027.t1 27587248 27588150
chr_1 g13027 g13027.t1 exon g13027.t1.exon1 27587248 27588150
chr_1 g13027 g13027.t1 cds g13027.t1.CDS1 27587248 27588150
chr_1 g13027 g13027.t1 TTS g13027.t1 NA NA

Sequences

>g13027.t1 Gene=g13027 Length=903
ATGCTTAAAGTAGTTGAAAATAAAATTTATGAGAGATTAAAGTCAAATAACGATAATTCA
TTTTATTTATTTGACATCAATGACATTCGAGAAAAGGTCAAATACTGGAAAGTAAAATTA
CCAAGAGTCGAGCCTTTTTTTGCAGTTAAATGTAACTATAATCGTGATATATTGATTGCT
ATCGATAAACTTGGACTTGGTTTTGAATGTGCTTCAAAAGGAGAAGTTGAAAAAGTTCTT
GAGTTAAAAATTGATCCTCAAAGAATTATTTATTCTCATACAGTGAAACAATTGTCTCAT
TTGCAATATTGTGCAGAGAAAAAAGTCAGTAAAATGACCTTTGATTCAAGTGCAGAACTT
TTAAGAATCAAAAAAAATTATCCAGACGCTGAAGTTTTTTTGAGAATTCGAATTGATAAG
AAAAATAGCACGTGTGCAGCTGATGTAAAATTTGGATGCGATATCGAACAAGAGGCTCTT
GAACTTATAAAAATGTGCTGCGATTTAAAAATGGATTTGATTGGCTTTAATTTTCACATT
GGCTCAATTACTGAGGATTTTCAAATTTATGAAAAGGCTTTGACTGAAGTTAGTAAATTA
TTTGACAAAGCTTCTTCTTTAGGTTTCCATCTTAATTTCATTAACATTGGTGGAGGATTT
TATGGAGAAAATAAAGAATGTTTGGACAATTACGTTGATCACATTAATAAAGCAATTGAT
ACACATTTTCCAAACATAAATTTAATTGTTGCAGAACCTGGAAGATATTTTGTGGAATCA
GCTGGAGTACTAGCTACACAAATTATTCTAAAGCGCATTTCTGTTGATGGACATGTTCAT
TATTATATTAATGAAGGGGTTTTCCTTTCCTTTCTTTTTACACTTGATTTATGGAAAAAC
TAA

>g13027.t1 Gene=g13027 Length=300
MLKVVENKIYERLKSNNDNSFYLFDINDIREKVKYWKVKLPRVEPFFAVKCNYNRDILIA
IDKLGLGFECASKGEVEKVLELKIDPQRIIYSHTVKQLSHLQYCAEKKVSKMTFDSSAEL
LRIKKNYPDAEVFLRIRIDKKNSTCAADVKFGCDIEQEALELIKMCCDLKMDLIGFNFHI
GSITEDFQIYEKALTEVSKLFDKASSLGFHLNFINIGGGFYGENKECLDNYVDHINKAID
THFPNINLIVAEPGRYFVESAGVLATQIILKRISVDGHVHYYINEGVFLSFLFTLDLWKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g13027.t1 Gene3D G3DSA:2.40.37.10 Lyase 15 291 3.4E-86
14 g13027.t1 Gene3D G3DSA:3.20.20.10 Alanine racemase 27 257 3.4E-86
2 g13027.t1 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 6 292 1.3E-90
3 g13027.t1 PANTHER PTHR11482:SF6 ORNITHINE DECARBOXYLASE 1-RELATED 6 292 1.3E-90
6 g13027.t1 PRINTS PR01182 Ornithine decarboxylase signature 19 43 1.5E-28
7 g13027.t1 PRINTS PR01182 Ornithine decarboxylase signature 45 72 1.5E-28
11 g13027.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 47 65 2.2E-22
10 g13027.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 67 79 2.2E-22
5 g13027.t1 PRINTS PR01182 Ornithine decarboxylase signature 89 113 1.5E-28
4 g13027.t1 PRINTS PR01182 Ornithine decarboxylase signature 119 141 1.5E-28
8 g13027.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 170 183 2.2E-22
9 g13027.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 249 268 2.2E-22
1 g13027.t1 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 27 258 8.3E-66
13 g13027.t1 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. 47 65 -
12 g13027.t1 SUPERFAMILY SSF51419 PLP-binding barrel 20 261 9.98E-58

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