General information for g2888.t1
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.t1 | TTS | g2888.t1 | 20914377 | 20914377 |
| chr_3 | g2888 | g2888.t1 | isoform | g2888.t1 | 20914433 | 20916054 |
| chr_3 | g2888 | g2888.t1 | exon | g2888.t1.exon1 | 20914433 | 20914685 |
| chr_3 | g2888 | g2888.t1 | cds | g2888.t1.CDS1 | 20914433 | 20914685 |
| chr_3 | g2888 | g2888.t1 | exon | g2888.t1.exon2 | 20914735 | 20915188 |
| chr_3 | g2888 | g2888.t1 | cds | g2888.t1.CDS2 | 20914735 | 20915188 |
| chr_3 | g2888 | g2888.t1 | exon | g2888.t1.exon3 | 20915258 | 20915341 |
| chr_3 | g2888 | g2888.t1 | cds | g2888.t1.CDS3 | 20915258 | 20915341 |
| chr_3 | g2888 | g2888.t1 | exon | g2888.t1.exon4 | 20915409 | 20915784 |
| chr_3 | g2888 | g2888.t1 | cds | g2888.t1.CDS4 | 20915409 | 20915784 |
| chr_3 | g2888 | g2888.t1 | exon | g2888.t1.exon5 | 20915851 | 20916054 |
| chr_3 | g2888 | g2888.t1 | cds | g2888.t1.CDS5 | 20915851 | 20916054 |
| chr_3 | g2888 | g2888.t1 | TSS | g2888.t1 | 20916112 | 20916112 |
Sequences
>g2888.t1 Gene=g2888 Length=1371
ATGAGCGAAGAAGTGTCAAAAATTGAAAAGAAAGTAACATTCGAGGAAATTGAGAAGACA
ATGAAACGTGCATCAATTTCTGACATTGCTGAGACGGTTGAAGATCCATTTTGTGATGAA
CGTAACCCAAGAATTATAACTTTTCAAGATGTATGTCAAGCAGCTTTCATGATTCGTGGT
GGCGTCGAAACAACACCTTGTTCCCGATCGCATTTGAGTGAGTCATGCGGAATGGAAATA
TATTTAAAAAAAGAATTTTTGCAATTCACGGGTAGCTTCAAAGAGCGTGGAGCTAGAAAT
GCCTTACTTCATTTAACACCCGAACAAAAAAAAAATGGAGTTGTATCAGCGTCGTTAGGC
AATCATGCACAAGCTATTGCTTATCATGGAATGAAACTCAATATTCCTGTAACTGTGGTG
ATGCCGAAAGAAGCTTCAATTATGAAGATACAAAAATGTAGAAACTTTAAAGCAAATGTT
ATCGTTCAAGGTTCTGATATGGCAGCTGCAAAAAAAATTGCTATGGAATTGTCTCGAGAT
AAAGGAATGCCCTATATTAATGGCTATGATCATCCATACATAATGGCTGGACAAGGAACG
ATTGGACTAGAAATTGTAGAGCAATGCGAGGGAGCGGATGCAGTTATAGTTCCTGTTGGC
GGAGGTGGTTTAATTGCTGGAATTGCAACTGCTATAAAGACTTTATCACCAAATACAAAA
ATTATTGGTGTTGAAAGCAATAAATGCCCATCATTTTCAAAAGCCTTAGAAAATGGAGGA
CCAATTTACACAAAAAATCATGCCACTTTAGCTGATGGTCTTGCTGTGCCAAAAGTAGGT
GTGAACGCTTATGCAACAATTGTGCCTCTTTTAGATAAAATGATTGTCGTAAAAGAAGAA
TGGATTGCCCTTGCAATTTTAAGAATGGTTGAGCTTGAAAAGTGTGTCGTAGAGGGTGCA
GGTGCAGCTGGTTTAGCTGCAATTTTAGCTGGGCATTTGGATGAATATAAAGGAAAGAAA
GTTGTTTTATTGGTATGCGGTGGAAATATTGATACAACAGCTTTCGGTCGTTGTCTTGAA
AGAGGAATGGCAGCTGAAGGGCGTCTTATTAGATTTAGTGTAACGGTGAGTGATCGACCA
GGTGGAATTTCGGAATTATGCAAACTCATTTATACATATGGTGTTAGCATAAAAGATATT
TATCATGAACGTGCCTTTTTAAAAGACGTTTATTCAGTTGAAGTAAAAATTGTTGCTGAA
ACTGCAGATTGGGACACGAGTCAACAGTTGAAGAAAAGGTTACATGAAGTCTATGATCAT
GTTGTATTTAATGATGTACCAATGGCAATTCATAAAGCAGAAGCTTTATAA
>g2888.t1 Gene=g2888 Length=456
MSEEVSKIEKKVTFEEIEKTMKRASISDIAETVEDPFCDERNPRIITFQDVCQAAFMIRG
GVETTPCSRSHLSESCGMEIYLKKEFLQFTGSFKERGARNALLHLTPEQKKNGVVSASLG
NHAQAIAYHGMKLNIPVTVVMPKEASIMKIQKCRNFKANVIVQGSDMAAAKKIAMELSRD
KGMPYINGYDHPYIMAGQGTIGLEIVEQCEGADAVIVPVGGGGLIAGIATAIKTLSPNTK
IIGVESNKCPSFSKALENGGPIYTKNHATLADGLAVPKVGVNAYATIVPLLDKMIVVKEE
WIALAILRMVELEKCVVEGAGAAGLAAILAGHLDEYKGKKVVLLVCGGNIDTTAFGRCLE
RGMAAEGRLIRFSVTVSDRPGGISELCKLIYTYGVSIKDIYHERAFLKDVYSVEVKIVAE
TADWDTSQQLKKRLHEVYDHVVFNDVPMAIHKAEAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2888.t1 | CDD | cd01562 | Thr-dehyd | 48 | 351 | 0 |
| 8 | g2888.t1 | CDD | cd04886 | ACT_ThrD-II-like | 372 | 443 | 0 |
| 5 | g2888.t1 | Gene3D | G3DSA:3.40.50.1100 | - | 52 | 352 | 0 |
| 6 | g2888.t1 | Gene3D | G3DSA:3.40.50.1100 | - | 93 | 189 | 0 |
| 2 | g2888.t1 | PANTHER | PTHR48078:SF12 | PROTEIN CBG07184 | 27 | 440 | 0 |
| 3 | g2888.t1 | PANTHER | PTHR48078 | THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED | 27 | 440 | 0 |
| 1 | g2888.t1 | Pfam | PF00291 | Pyridoxal-phosphate dependent enzyme | 60 | 347 | 0 |
| 4 | g2888.t1 | SUPERFAMILY | SSF53686 | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 21 | 394 | 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 transcript has been annotated with K01754 (threonine dehydratase)
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