General information for g16088.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable low-specificity L-threonine aldolase 1.
Parent gene
- The parent gene g16088 is located on chr_4: 8103365..8104037 (+ 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_4 | g16088 | g16088.t2 | TSS | g16088.t2 | 8102255 | 8102255 |
| chr_4 | g16088 | g16088.t2 | isoform | g16088.t2 | 8102310 | 8104037 |
| chr_4 | g16088 | g16088.t2 | exon | g16088.t2.exon1 | 8102310 | 8102387 |
| chr_4 | g16088 | g16088.t2 | exon | g16088.t2.exon2 | 8102570 | 8102738 |
| chr_4 | g16088 | g16088.t2 | exon | g16088.t2.exon3 | 8102800 | 8102831 |
| chr_4 | g16088 | g16088.t2 | exon | g16088.t2.exon4 | 8103033 | 8103234 |
| chr_4 | g16088 | g16088.t2 | exon | g16088.t2.exon5 | 8103359 | 8104037 |
| chr_4 | g16088 | g16088.t2 | cds | g16088.t2.CDS1 | 8103435 | 8104037 |
| chr_4 | g16088 | g16088.t2 | TTS | g16088.t2 | 8104105 | 8104105 |
Sequences
>g16088.t2 Gene=g16088 Length=1160
ATGTCAATTTATCGCAGAGTTTTTGATGATGCTTCTTTAAAAAACTATAGAATTGTCGAT
TTAAGAAGTGATACTTTATCAGTTCCAACAGATGAAATGAGAAAAGCAATGTTTGAATCT
GAAATTGGTGATGATGTTTATGGTGAAGATCCAACTGTTAATAAACTTGAAGTTAAAGTC
GCTGAATTATTAGGAAAAGAAGCTGCAGTTTTTGTTCCATCTGGAACTATGGGAAATTTG
CTTGCAATCATGGTCCATTGTGATAAGCGAGGCTCTGAGGTCATGTGCGGCAGTCTTAGT
CATGTCTTTTGTTATGAACAAGGTTCAGCTTCATCACTTGCTGGAGTTTTTGTTCATAAA
TTGGAAAACAATGAAGATGGAACATTTTCAATTGAAGCAGTGAAAAAATTAGCCAGAGGT
TCTGATATTCATGAACCAGTAACTCAATTAGTTGTTGTTGAGAATACACACAATATGGCA
GAGGTGGAAAAGTTTTGCCATTAAACTGGATTGAAGAATTGTCAAAAGTTTGCAAAGATA
AAAACCTAAAACTTCACATGGATGGAGCTCGTGTTTTTAGTGCAGCTGAATATCTTAAAG
TTCCAGTTTCTCGTGTAGTTCGTGATGTTGATTCAATATCATTTTGTTTGAGTAAAAATC
TTTGCTGTCCTGTTGGTTCATTGCTTGTTGGCAAAAAAGAATTTGTTGAACAAGCAAGAA
GATTTCGAAAAGCACTTGGTGGTGGAATGAGACAAGTTGGATTTTTGGCAGCTGCTGGAA
TGTTTGCTCTTGATAATATTGTGCCGAAATTGAAATTTGATCATGAACATGCAAAACAAC
TTGCTGCTGCTGTTGATGAGCTTAAAAGTAAAATTTTCTATGTTGACGTCAAAAATTTAC
ATAGCAATATTTTGATGATAAAAGTTGCTGATAATGATAAAAACATTACAGCTTTAGATT
TGAGTAATCGTTTGGTAGAAGTAAAAGATGAAGAAATTGAAAATGGAATATGTGATGAAC
AGAAGAAAGGAATAATTGTCAAATCAAGCTGCAAAAATTTGCAAACATTGCGTGTTGTTT
TTTATCATCAAATTACTGATGAAATGACAAATTTATTAGTCAAAAAAGTTTCATACGTCA
TTAAGGAATTTGAAAAGTGA
>g16088.t2 Gene=g16088 Length=200
MDGARVFSAAEYLKVPVSRVVRDVDSISFCLSKNLCCPVGSLLVGKKEFVEQARRFRKAL
GGGMRQVGFLAAAGMFALDNIVPKLKFDHEHAKQLAAAVDELKSKIFYVDVKNLHSNILM
IKVADNDKNITALDLSNRLVEVKDEEIENGICDEQKKGIIVKSSCKNLQTLRVVFYHQIT
DEMTNLLVKKVSYVIKEFEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g16088.t2 | Gene3D | G3DSA:3.40.640.10 | - | 1 | 80 | 0 |
| 5 | g16088.t2 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 81 | 196 | 0 |
| 2 | g16088.t2 | PANTHER | PTHR48097:SF9 | L-THREONINE ALDOLASE | 1 | 199 | 0 |
| 3 | g16088.t2 | PANTHER | PTHR48097 | L-THREONINE ALDOLASE-RELATED | 1 | 199 | 0 |
| 1 | g16088.t2 | Pfam | PF01212 | Beta-eliminating lyase | 1 | 115 | 0 |
| 4 | g16088.t2 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 1 | 196 | 0 |
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:0016829 | lyase activity | MF |
| GO:0006520 | cellular amino acid metabolic process | BP |
| GO:0003824 | catalytic activity | MF |
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. There were no conditions that were differentially expressed