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 g8778 g8778.t1 TSS g8778.t1 33097417 33097417
chr_2 g8778 g8778.t1 isoform g8778.t1 33099373 33100741
chr_2 g8778 g8778.t1 exon g8778.t1.exon1 33099373 33100087
chr_2 g8778 g8778.t1 cds g8778.t1.CDS1 33099373 33100087
chr_2 g8778 g8778.t1 exon g8778.t1.exon2 33100149 33100741
chr_2 g8778 g8778.t1 cds g8778.t1.CDS2 33100149 33100741
chr_2 g8778 g8778.t1 TTS g8778.t1 33100879 33100879

Sequences

>g8778.t1 Gene=g8778 Length=1308
ATGAAATTCAGTGCAAATGAAGATTGCATCCAAGTAATTGATGAAACTACAAATGTAGTA
AACATCATTAATGAATTGACAATGCATGGAACAACAAACAATGAGGATCCATTTTACATT
TTTGACATTGGTGACGTTGTAAAAAAGCATCAGTCATGGATAGAAAGAATGCCGCGTGTA
ATTCCACACTATGCTGTTAAATGCAATGATAATGATGTTGTATTAGCGACACTAGCAGCT
CTTGGAACTTCTTTCGATTGCGCATCAAAAGTAGAAATCAGTAAAGTTCTTAGCTTGGGT
GTTCAACCTGAAAGAATTATCTATGCCAATCCATGCAAGAGCAAATCATCAATCATTTAT
GCTAGAGAAGTTGGCGTAAAAACGATGACATTTGATTGTGACATTGAACTGCAGAAGATC
AAAAAACTTTTTCCTGACGCAAATTTAGTTTTACGTATTCGTTGTGAAGCTGAAATTGCT
CAATGCGCACTTGGCAAAAAGTTTGGTTGCGATCCTGTTATTGAAGCTCCAAAACTTCTT
AAGACTGCTCGCAGTTTAAATTTGAATGTTGTTGGCATTAGTTTTCATGTTGGCTCTGGA
TGTGCAGATTTTCCAATATATCGAAAAGCACTGGGATTCTGTAAAGTTCTCTTCATGAAA
GCTGAAGAACTTGGCTATAATCTCACAATTGTTGACATTGGTGGTGGCTTTCCTGGTGAT
AATGATAAAAGTATTGATGAAGTTTCAATCATTATCAATCAGAGCCTAGAAGAATATTTT
CCAGAAAAGCACGTACGTGTCATTGCAGAACCTGGACGTTTTTATGTCGCTTCTGCTTTT
ACATTAATCACAAATGTACATTCGAAGAAAAACATTTACAATCCATTAAGCGATGAAATT
GAGAGCACTATGCTTTATATCAATGATGGTGTTTATGCTTCATTTAATTGTCTCCTATAT
GATCATCAAATTGTAAAACCTAAATTATTAAAAGACCACAGTGAGACTGAAAAGACTATA
AAGACAACAATTTTCGGCCCAACGTGTGATGCACTTGATGAAATCATTGTAGGTGCAAAT
ATGCCTGAATCAATTGATCTTGGGGATTTTATTTACTTTGAAAATATGGGAGCTTATACA
TTGCCTGTTGCATCACCATTCAATGGTTTTCCACTTCCAAAAGTTTATCATTTCATTGAA
CGCGATATGTGGCAAATGGTTCGTTCAATGATCCCTGTGGAAGCTAACGACAGATTCATA
GAAGATTTCATTGGAAAAACTATTGAAATTGTCTCAACTACCGCCTAA

>g8778.t1 Gene=g8778 Length=435
MKFSANEDCIQVIDETTNVVNIINELTMHGTTNNEDPFYIFDIGDVVKKHQSWIERMPRV
IPHYAVKCNDNDVVLATLAALGTSFDCASKVEISKVLSLGVQPERIIYANPCKSKSSIIY
AREVGVKTMTFDCDIELQKIKKLFPDANLVLRIRCEAEIAQCALGKKFGCDPVIEAPKLL
KTARSLNLNVVGISFHVGSGCADFPIYRKALGFCKVLFMKAEELGYNLTIVDIGGGFPGD
NDKSIDEVSIIINQSLEEYFPEKHVRVIAEPGRFYVASAFTLITNVHSKKNIYNPLSDEI
ESTMLYINDGVYASFNCLLYDHQIVKPKLLKDHSETEKTIKTTIFGPTCDALDEIIVGAN
MPESIDLGDFIYFENMGAYTLPVASPFNGFPLPKVYHFIERDMWQMVRSMIPVEANDRFI
EDFIGKTIEIVSTTA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g8778.t1 CDD cd00622 PLPDE_III_ODC 35 398 0.0
22 g8778.t1 Gene3D G3DSA:2.40.37.10 Lyase 22 391 5.2E-148
21 g8778.t1 Gene3D G3DSA:3.20.20.10 Alanine racemase 44 275 5.2E-148
3 g8778.t1 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE 23 408 1.7E-146
4 g8778.t1 PANTHER PTHR11482:SF6 ORNITHINE DECARBOXYLASE 1-RELATED 23 408 1.7E-146
8 g8778.t1 PRINTS PR01182 Ornithine decarboxylase signature 36 60 6.0E-59
5 g8778.t1 PRINTS PR01182 Ornithine decarboxylase signature 62 89 6.0E-59
16 g8778.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 64 82 4.3E-33
13 g8778.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 84 96 4.3E-33
10 g8778.t1 PRINTS PR01182 Ornithine decarboxylase signature 106 130 6.0E-59
7 g8778.t1 PRINTS PR01182 Ornithine decarboxylase signature 136 158 6.0E-59
12 g8778.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 187 200 4.3E-33
14 g8778.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 267 286 4.3E-33
6 g8778.t1 PRINTS PR01182 Ornithine decarboxylase signature 309 322 6.0E-59
11 g8778.t1 PRINTS PR01182 Ornithine decarboxylase signature 343 353 6.0E-59
9 g8778.t1 PRINTS PR01182 Ornithine decarboxylase signature 364 377 6.0E-59
15 g8778.t1 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature 377 390 4.3E-33
1 g8778.t1 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain 44 277 2.9E-75
2 g8778.t1 Pfam PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain 278 377 6.1E-17
19 g8778.t1 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. 64 82 -
20 g8778.t1 ProSitePatterns PS00879 Orn/DAP/Arg decarboxylases family 2 signature 2. 221 238 -
17 g8778.t1 SUPERFAMILY SSF51419 PLP-binding barrel 36 279 4.3E-63
18 g8778.t1 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like 249 407 9.0E-39

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.

Raw TPM values