General information for g2888.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative L-threonine ammonia-lyase.
Parent gene
- The parent gene g2888 is located on chr_3: 20914433..20916054 (- 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_3 | g2888 | g2888.t7 | TTS | g2888.t7 | 20914377 | 20914377 |
| chr_3 | g2888 | g2888.t7 | isoform | g2888.t7 | 20914433 | 20915426 |
| chr_3 | g2888 | g2888.t7 | exon | g2888.t7.exon1 | 20914433 | 20914685 |
| chr_3 | g2888 | g2888.t7 | cds | g2888.t7.CDS1 | 20914433 | 20914685 |
| chr_3 | g2888 | g2888.t7 | exon | g2888.t7.exon2 | 20914735 | 20915188 |
| chr_3 | g2888 | g2888.t7 | cds | g2888.t7.CDS2 | 20914735 | 20915188 |
| chr_3 | g2888 | g2888.t7 | exon | g2888.t7.exon3 | 20915258 | 20915341 |
| chr_3 | g2888 | g2888.t7 | cds | g2888.t7.CDS3 | 20915258 | 20915339 |
| chr_3 | g2888 | g2888.t7 | exon | g2888.t7.exon4 | 20915409 | 20915426 |
| chr_3 | g2888 | g2888.t7 | TSS | g2888.t7 | 20916112 | 20916112 |
Sequences
>g2888.t7 Gene=g2888 Length=809
GCTATGATCATCCATACATAATGGCTGGACAAGGAACGATTGGACTAGAAATTGTAGAGC
AATGCGAGGGAGCGGATGCAGTTATAGTTCCTGTTGGCGGAGGTGGTTTAATTGCTGGAA
TTGCAACTGCTATAAAGACTTTATCACCAAATACAAAAATTATTGGTGTTGAAAGCAATA
AATGCCCATCATTTTCAAAAGCCTTAGAAAATGGAGGACCAATTTACACAAAAAATCATG
CCACTTTAGCTGATGGTCTTGCTGTGCCAAAAGTAGGTGTGAACGCTTATGCAACAATTG
TGCCTCTTTTAGATAAAATGATTGTCGTAAAAGAAGAATGGATTGCCCTTGCAATTTTAA
GAATGGTTGAGCTTGAAAAGTGTGTCGTAGAGGGTGCAGGTGCAGCTGGTTTAGCTGCAA
TTTTAGCTGGGCATTTGGATGAATATAAAGGAAAGAAAGTTGTTTTATTGGTATGCGGTG
GAAATATTGATACAACAGCTTTCGGTCGTTGTCTTGAAAGAGGAATGGCAGCTGAAGGGC
GTCTTATTAGATTTAGTGTAACGGTGAGTGATCGACCAGGTGGAATTTCGGAATTATGCA
AACTCATTTATACATATGGTGTTAGCATAAAAGATATTTATCATGAACGTGCCTTTTTAA
AAGACGTTTATTCAGTTGAAGTAAAAATTGTTGCTGAAACTGCAGATTGGGACACGAGTC
AACAGTTGAAGAAAAGGTTACATGAAGTCTATGATCATGTTGTATTTAATGATGTACCAA
TGGCAATTCATAAAGCAGAAGCTTTATAA
>g2888.t7 Gene=g2888 Length=262
MAGQGTIGLEIVEQCEGADAVIVPVGGGGLIAGIATAIKTLSPNTKIIGVESNKCPSFSK
ALENGGPIYTKNHATLADGLAVPKVGVNAYATIVPLLDKMIVVKEEWIALAILRMVELEK
CVVEGAGAAGLAAILAGHLDEYKGKKVVLLVCGGNIDTTAFGRCLERGMAAEGRLIRFSV
TVSDRPGGISELCKLIYTYGVSIKDIYHERAFLKDVYSVEVKIVAETADWDTSQQLKKRL
HEVYDHVVFNDVPMAIHKAEAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2888.t7 | CDD | cd04886 | ACT_ThrD-II-like | 178 | 249 | 0 |
| 5 | g2888.t7 | Gene3D | G3DSA:3.40.50.1100 | - | 1 | 175 | 0 |
| 2 | g2888.t7 | PANTHER | PTHR48078:SF12 | PROTEIN CBG07184 | 1 | 246 | 0 |
| 3 | g2888.t7 | PANTHER | PTHR48078 | THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED | 1 | 246 | 0 |
| 1 | g2888.t7 | Pfam | PF00291 | Pyridoxal-phosphate dependent enzyme | 1 | 153 | 0 |
| 4 | g2888.t7 | SUPERFAMILY | SSF53686 | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 1 | 200 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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