Gene loci information

Transcript annotation

  • This transcript has been annotated as L-threonine 3-dehydrogenase, mitochondrial.

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_3 g421 g421.t1 TTS g421.t1 3301618 3301618
chr_3 g421 g421.t1 isoform g421.t1 3301722 3305232
chr_3 g421 g421.t1 exon g421.t1.exon1 3301722 3301861
chr_3 g421 g421.t1 cds g421.t1.CDS1 3301722 3301861
chr_3 g421 g421.t1 exon g421.t1.exon2 3301920 3302074
chr_3 g421 g421.t1 cds g421.t1.CDS2 3301920 3302074
chr_3 g421 g421.t1 exon g421.t1.exon3 3302488 3302608
chr_3 g421 g421.t1 cds g421.t1.CDS3 3302488 3302608
chr_3 g421 g421.t1 exon g421.t1.exon4 3302676 3302794
chr_3 g421 g421.t1 cds g421.t1.CDS4 3302676 3302794
chr_3 g421 g421.t1 exon g421.t1.exon5 3302849 3303239
chr_3 g421 g421.t1 cds g421.t1.CDS5 3302849 3303239
chr_3 g421 g421.t1 exon g421.t1.exon6 3305121 3305232
chr_3 g421 g421.t1 cds g421.t1.CDS6 3305121 3305232
chr_3 g421 g421.t1 TSS g421.t1 3305367 3305367

Sequences

>g421.t1 Gene=g421 Length=1038
ATGTCCGGTATACGATTTTCAAAATTACTTTATAGGCCGCTATTGCTAAATAATAGTCAT
TTATTATTGAGGCACTATTCATTACAGCGTTCACCCAGAATCCTCATCACAGGTGGTTTG
GGTCAACTCGGGACACAATGTGCAAAGCTCTTAAGAGCAAAATATGGAAGAGACAATGTC
ATATTGTCTGACATTGTTAAACCTAGTGATGAAATAATTGATGCCGGACCCTACCTCTTT
GCTGATATTTTAGACTTTAAAGGTCTTCAAAAAGCAGTTGTTTCTCATCGCATCGATTGG
ATAATTCATTTCTCAGCTTTACTTAGTGCAATTGGTGAACAAAATGTGTCACTTGCTATT
CGAGTAAATATAGAAGGCATGCATAATATGGTTGAGTTAGCAAAGCAATATAAACTGAGA
ATTTTCGTACCTTCAACAATTGGTGCTTTCGGTCCAGATTCTCCTCGAAATCCTACGCCC
AATTTGACTATTCAGAGGCCAAGAACAATCTATGGAGTTTCAAAAGTTCATGCAGAATTG
ATGGGCGAGTATTATCATCACAAATTTGGAACTGATTTTCGTTGTTTGAGATTTCCTGGT
GTAATTAGTGCTGATCCTCCTGGTGGTGGTACAACTGATTATGCTGTCGCTATTTTCTAT
GATGCATTGAAAAAAGGTCATTATAATTGCTATCTTAAACCTGACACAATGTTGCCAATG
ATTCACATTAAAGATTGTTTGAGATCTTTAATGGAATTTATGGCTGTCCCTGAAGAGAAA
TTAAAACGAAGAGTTTATAATGTGACAGCAATGTCATTTACTCCTGAAGAGTTAGCTGAA
AAAATTTCAAAGCATGTGCCACAACTTTCAATATCTTATAATCCAGATAGTCGTCAAGCA
ATTGCTGATGATTGGCCACAGGTTTTTGATGATTCAGAAGCAAGAGCTGATTGGGGATGG
AAGCATGAATATGATTTAGATAGACTTGTTGTTGATATTCTTAAAGAAGTTCGTGGACGT
TTAAATATGAAACATTAA

>g421.t1 Gene=g421 Length=345
MSGIRFSKLLYRPLLLNNSHLLLRHYSLQRSPRILITGGLGQLGTQCAKLLRAKYGRDNV
ILSDIVKPSDEIIDAGPYLFADILDFKGLQKAVVSHRIDWIIHFSALLSAIGEQNVSLAI
RVNIEGMHNMVELAKQYKLRIFVPSTIGAFGPDSPRNPTPNLTIQRPRTIYGVSKVHAEL
MGEYYHHKFGTDFRCLRFPGVISADPPGGGTTDYAVAIFYDALKKGHYNCYLKPDTMLPM
IHIKDCLRSLMEFMAVPEEKLKRRVYNVTAMSFTPEELAEKISKHVPQLSISYNPDSRQA
IADDWPQVFDDSEARADWGWKHEYDLDRLVVDILKEVRGRLNMKH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g421.t1 CDD cd05272 TDH_SDR_e 33 337 0
4 g421.t1 Gene3D G3DSA:3.40.50.720 - 25 344 0
2 g421.t1 PANTHER PTHR42687 L-THREONINE 3-DEHYDROGENASE 26 341 0
1 g421.t1 Pfam PF01370 NAD dependent epimerase/dehydratase family 34 268 0
3 g421.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 28 340 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:0003824 catalytic 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.

Raw TPM values