Gene loci information

Transcript annotation

  • This transcript has been annotated as D-amino-acid oxidase.

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 g13018 g13018.t3 isoform g13018.t3 27536374 27537757
chr_1 g13018 g13018.t3 exon g13018.t3.exon1 27536374 27536713
chr_1 g13018 g13018.t3 cds g13018.t3.CDS1 27536620 27536713
chr_1 g13018 g13018.t3 exon g13018.t3.exon2 27536782 27537504
chr_1 g13018 g13018.t3 cds g13018.t3.CDS2 27536782 27537504
chr_1 g13018 g13018.t3 exon g13018.t3.exon3 27537564 27537757
chr_1 g13018 g13018.t3 cds g13018.t3.CDS3 27537564 27537757
chr_1 g13018 g13018.t3 TSS g13018.t3 NA NA
chr_1 g13018 g13018.t3 TTS g13018.t3 NA NA

Sequences

>g13018.t3 Gene=g13018 Length=1257
ATGAAGAAAATTTATATTGTCGGTGCAGGCATCTGTGGAATCTCAGCTGCTGTGCAAATT
GCAGAAAATTTCAAGAATCAAAATGTTGAAGTGATTGTTGTAGCTGAGAAATTTACACCA
AATACAACAAGTGATTTAGTTGCTGGCCTATGGGGTCCTTATCTAATGGGCAGCACTCCA
GAGCACAAAATTGTTCAATGGTCGAAAACGACACACGAATATTTTCATCATTTATGGTTG
AATGGATTGGCAGAAGAAGCTGGCATAACGATGATTCCTTGCTATCGTTTGTCAGCTGAA
GAAGAAATACAAAATCCATGCTGGAAAAATATTGTTTTTGGCTTTCGTGAATTGACTTCT
CAAGAGATTTCTAAAATGAGTCGTGAACATCGTCGTAAATATTTGAGTGGAAGCAATTTT
GTCACATTTTGTTGCGAACCAATCAAATTTATACCTTTTATGACAAAGAGATTTATAAAA
GCAGGCGGAAAGTTAGAGACGAGAAAATTGCGTGACTTTGATGAATTGAAAGATGCTGAC
TTGATTGTCAACTGCACGGGATTAGGCGGAAAAGAGCTTGGCGATGAACAGCTCCATCCA
ATTAGAGGACAAATTACACGAGTTAGTGCACCTTGGATGTATTTTGTTATGATTGACGAT
AGCGATGATGGCAATTATATTATTCCAAATGCAGAATCAGTCGTGCTTGGTGGAACACAT
CAGTACAATGACTTTAATACAAAATTTTCAACATCAGATAATGACTTTATCATGAATGGC
TGCCAGCGAATGGTCAAAAGTCTTGAAAATGCCGAAAGACTAAGAGACATTGTTGGCTTA
AGACCTGGAAGGGATCAAGTGAGACTTGAAATTGTGCATGGCACGAATGGAAAAGCACCG
GTAATTCATAATGTAGGACATGGTGGATGCGGTGTGACATTATCCTGGGGTTGTGGACAA
GAAGTTTTAGAGAAAACTGTTGAAGTGATGAAAGGAATGTCAAAATTGTAAATTTGAAAT
TTCTTTTTGTATGAAAAATAATTTTGAAATAACCGTTAAAATTTGAAATTTCACTAACAT
AAATAAAAGCTTTTTTTGTACATAATTACGTAAAATTGAAAAATTTAAAATTCAAAAATT
AGTCAAATAAATCACAAAAATAAATGTATTTAAAGTATTTTATTTCATTATCTCTAATTG
GTTATGTCAAGATGATTCTGAGTTGTTAGAATAAATTTAAAATTACAAAAGTAAAAG

>g13018.t3 Gene=g13018 Length=336
MKKIYIVGAGICGISAAVQIAENFKNQNVEVIVVAEKFTPNTTSDLVAGLWGPYLMGSTP
EHKIVQWSKTTHEYFHHLWLNGLAEEAGITMIPCYRLSAEEEIQNPCWKNIVFGFRELTS
QEISKMSREHRRKYLSGSNFVTFCCEPIKFIPFMTKRFIKAGGKLETRKLRDFDELKDAD
LIVNCTGLGGKELGDEQLHPIRGQITRVSAPWMYFVMIDDSDDGNYIIPNAESVVLGGTH
QYNDFNTKFSTSDNDFIMNGCQRMVKSLENAERLRDIVGLRPGRDQVRLEIVHGTNGKAP
VIHNVGHGGCGVTLSWGCGQEVLEKTVEVMKGMSKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g13018.t3 Gene3D G3DSA:3.40.50.720 - 4 323 1.0E-87
6 g13018.t3 Gene3D G3DSA:3.30.9.10 - 89 283 1.0E-87
2 g13018.t3 PANTHER PTHR11530 D-AMINO ACID OXIDASE 1 335 1.3E-92
12 g13018.t3 PIRSF PIRSF000189 D-aa_oxidase 1 335 5.0E-79
1 g13018.t3 Pfam PF01266 FAD dependent oxidoreductase 4 322 1.4E-35
8 g13018.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
9 g13018.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
10 g13018.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
11 g13018.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 17 -
7 g13018.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 336 -
3 g13018.t3 SUPERFAMILY SSF51971 Nucleotide-binding domain 1 324 3.65E-20
4 g13018.t3 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain 198 284 3.14E-18

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:0046416 D-amino acid metabolic process BP
GO:0003884 D-amino-acid oxidase activity MF
GO:0055114 NA NA
GO:0071949 FAD binding MF
GO:0016491 oxidoreductase activity MF

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. There were no conditions that were differentially expressed