General information for g13018.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as D-amino-acid oxidase.
Parent gene
- The parent gene g13018 is located on chr_1: 27536624..27537757 (- strand)
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.t1 | TTS | g13018.t1 | 27528072 | 27528072 |
| chr_1 | g13018 | g13018.t1 | isoform | g13018.t1 | 27528850 | 27537757 |
| chr_1 | g13018 | g13018.t1 | exon | g13018.t1.exon1 | 27528850 | 27529117 |
| chr_1 | g13018 | g13018.t1 | cds | g13018.t1.CDS1 | 27528850 | 27529117 |
| chr_1 | g13018 | g13018.t1 | exon | g13018.t1.exon2 | 27536624 | 27536713 |
| chr_1 | g13018 | g13018.t1 | cds | g13018.t1.CDS2 | 27536624 | 27536713 |
| chr_1 | g13018 | g13018.t1 | exon | g13018.t1.exon3 | 27536782 | 27537504 |
| chr_1 | g13018 | g13018.t1 | cds | g13018.t1.CDS3 | 27536782 | 27537504 |
| chr_1 | g13018 | g13018.t1 | exon | g13018.t1.exon4 | 27537564 | 27537757 |
| chr_1 | g13018 | g13018.t1 | cds | g13018.t1.CDS4 | 27537564 | 27537757 |
| chr_1 | g13018 | g13018.t1 | TSS | g13018.t1 | NA | NA |
Sequences
>g13018.t1 Gene=g13018 Length=1275
ATGAAGAAAATTTATATTGTCGGTGCAGGCATCTGTGGAATCTCAGCTGCTGTGCAAATT
GCAGAAAATTTCAAGAATCAAAATGTTGAAGTGATTGTTGTAGCTGAGAAATTTACACCA
AATACAACAAGTGATTTAGTTGCTGGCCTATGGGGTCCTTATCTAATGGGCAGCACTCCA
GAGCACAAAATTGTTCAATGGTCGAAAACGACACACGAATATTTTCATCATTTATGGTTG
AATGGATTGGCAGAAGAAGCTGGCATAACGATGATTCCTTGCTATCGTTTGTCAGCTGAA
GAAGAAATACAAAATCCATGCTGGAAAAATATTGTTTTTGGCTTTCGTGAATTGACTTCT
CAAGAGATTTCTAAAATGAGTCGTGAACATCGTCGTAAATATTTGAGTGGAAGCAATTTT
GTCACATTTTGTTGCGAACCAATCAAATTTATACCTTTTATGACAAAGAGATTTATAAAA
GCAGGCGGAAAGTTAGAGACGAGAAAATTGCGTGACTTTGATGAATTGAAAGATGCTGAC
TTGATTGTCAACTGCACGGGATTAGGCGGAAAAGAGCTTGGCGATGAACAGCTCCATCCA
ATTAGAGGACAAATTACACGAGTTAGTGCACCTTGGATGTATTTTGTTATGATTGACGAT
AGCGATGATGGCAATTATATTATTCCAAATGCAGAATCAGTCGTGCTTGGTGGAACACAT
CAGTACAATGACTTTAATACAAAATTTTCAACATCAGATAATGACTTTATCATGAATGGC
TGCCAGCGAATGGTCAAAAGTCTTGAAAATGCCGAAAGACTAAGAGACATTGTTGGCTTA
AGACCTGGAAGGGATCAAGTGAGACTTGAAATTGTGCATGGCACGAATGGAAAAGCACCG
GTAATTCATAATGTAGGACATGGTGGATGCGGTGTGACATTATCCTGGGGTTGTGGACAA
GAAGTTTTAGAGAAAACTGTTGAAGTGATGAAAGGAATGTCAAAATTATTTCATATTGCT
ACTTTTGCAATTCTTCAAGTAAATTTAGTTTATTCAGCAGTTTTAACCTGCAATTCGACA
ACACCACCATGCGTCGTCACTTCAATCACTCCAGTAACTTCACCTTATGAATTGATCACA
ATTGATGGACAACCATCAAATTATATTGATGAGACAACGACAGATTTATCCTTCAATGCA
CCAAATATTTTAAATTATGTTCCAACAAACGTTTTCAATATTTTTCCAAAAACTCAATCA
AATTATTTTGTCTAA
>g13018.t1 Gene=g13018 Length=424
MKKIYIVGAGICGISAAVQIAENFKNQNVEVIVVAEKFTPNTTSDLVAGLWGPYLMGSTP
EHKIVQWSKTTHEYFHHLWLNGLAEEAGITMIPCYRLSAEEEIQNPCWKNIVFGFRELTS
QEISKMSREHRRKYLSGSNFVTFCCEPIKFIPFMTKRFIKAGGKLETRKLRDFDELKDAD
LIVNCTGLGGKELGDEQLHPIRGQITRVSAPWMYFVMIDDSDDGNYIIPNAESVVLGGTH
QYNDFNTKFSTSDNDFIMNGCQRMVKSLENAERLRDIVGLRPGRDQVRLEIVHGTNGKAP
VIHNVGHGGCGVTLSWGCGQEVLEKTVEVMKGMSKLFHIATFAILQVNLVYSAVLTCNST
TPPCVVTSITPVTSPYELITIDGQPSNYIDETTTDLSFNAPNILNYVPTNVFNIFPKTQS
NYFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13018.t1 | Gene3D | G3DSA:3.40.50.720 | - | 4 | 323 | 2.4E-87 |
| 6 | g13018.t1 | Gene3D | G3DSA:3.30.9.10 | - | 89 | 283 | 2.4E-87 |
| 2 | g13018.t1 | PANTHER | PTHR11530 | D-AMINO ACID OXIDASE | 1 | 335 | 2.7E-92 |
| 1 | g13018.t1 | Pfam | PF01266 | FAD dependent oxidoreductase | 4 | 322 | 3.2E-35 |
| 8 | g13018.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 9 | g13018.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 10 | g13018.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 11 | g13018.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 7 | g13018.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 424 | - |
| 3 | g13018.t1 | SUPERFAMILY | SSF51971 | Nucleotide-binding domain | 1 | 324 | 8.24E-20 |
| 4 | g13018.t1 | SUPERFAMILY | SSF54373 | FAD-linked reductases, C-terminal domain | 198 | 284 | 4.71E-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
- This transcript has been annotated with K00273 (D-amino-acid oxidase)
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