Gene loci information

Transcript annotation

  • This transcript has been annotated as Trans-1-2-dihydrobenzene-1,2-diol dehydrogenase.

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_4 g17251 g17251.t1 TTS g17251.t1 12946119 12946119
chr_4 g17251 g17251.t1 isoform g17251.t1 12946246 12947879
chr_4 g17251 g17251.t1 exon g17251.t1.exon1 12946246 12946503
chr_4 g17251 g17251.t1 cds g17251.t1.CDS1 12946246 12946503
chr_4 g17251 g17251.t1 exon g17251.t1.exon2 12946569 12946815
chr_4 g17251 g17251.t1 cds g17251.t1.CDS2 12946569 12946815
chr_4 g17251 g17251.t1 exon g17251.t1.exon3 12946876 12947170
chr_4 g17251 g17251.t1 cds g17251.t1.CDS3 12946876 12947170
chr_4 g17251 g17251.t1 exon g17251.t1.exon4 12947672 12947879
chr_4 g17251 g17251.t1 cds g17251.t1.CDS4 12947672 12947879
chr_4 g17251 g17251.t1 TSS g17251.t1 12947946 12947946

Sequences

>g17251.t1 Gene=g17251 Length=1008
ATGTCTAAACCTTTACGTTGGGGTATTGTATCAGCTGGCAAAATCGCAAATGACTTTTGT
GCAGCTTTGTCAACATTTTCAAATGAAGAACATCAAGTTGTTGCAGTTGCAGCTCGCAAA
GAAGCTGATGCAAAAGAATTTGCCGAAACTTTTAACATTCCAAAATATTATGAAGGATAT
GAAAAATTGGCTAATGACAATGAAGTTGATGCTGTCTACATTGGCTCAATAAATACATGT
CATCTAGAAGACAGTATCATGATGCTCGATGCAGGCAAGCCAGTTTTATGTGAGAAACCT
TTTGCATTGAATGAAAAACAATCTGTTGAAATTTTTAATCGTGCAAAGGAGAAGAAACTT
TTCTGTATGGAAGCAGTTTGGTCACGATTTTTACCATCATATGAATACATGAGACATCGT
CTTGATAATAATGATTTTGGTGAAATCACAGAAGTTGAAATTGAATATGGAAAGGAAAAA
CTTGGAAAAATGGAAAGAGTTGTCAAAAAAGATCTTGGCGGTAGCATGTTGTTGGACATT
GGAAATTATGCGATTCAATTTGCTCAATTTGTTTTCCGCTCATATCCGACATCAATTAAA
GCAACTGGCAAATTGAATGATGATGGTGTTGATGTAGAAGCAGAAATTGAATTGAAATAT
TTAAATGGTGGCGTTGCTAAAATTAAGACTAGTGCCATAAACAATCTTAAAAATCAAGCT
AATATTTATGGCAGTAAAGGTTCAATGACTGTCGATCAATTTTGGGCTTGTACTTATTTG
ATCGACATTGATGGACATCCAAAAGAATGGAAGCTACCAGAGCCAAAGCAAGGCGAGTTT
GTATTTAATAACAGAGCTGGTTTAAGATTCCAAGCAGAAGAAACCAGAAGATGCATTAAT
GAAGGAAAACTTGAAAGTGATCTCATGCCTCAAAAGGAAACAATTGAAATTGCTCGCATT
CGTGATGAAATTCGCAAACAAATTGGTGTCAGATATGATGAAGATTAA

>g17251.t1 Gene=g17251 Length=335
MSKPLRWGIVSAGKIANDFCAALSTFSNEEHQVVAVAARKEADAKEFAETFNIPKYYEGY
EKLANDNEVDAVYIGSINTCHLEDSIMMLDAGKPVLCEKPFALNEKQSVEIFNRAKEKKL
FCMEAVWSRFLPSYEYMRHRLDNNDFGEITEVEIEYGKEKLGKMERVVKKDLGGSMLLDI
GNYAIQFAQFVFRSYPTSIKATGKLNDDGVDVEAEIELKYLNGGVAKIKTSAINNLKNQA
NIYGSKGSMTVDQFWACTYLIDIDGHPKEWKLPEPKQGEFVFNNRAGLRFQAEETRRCIN
EGKLESDLMPQKETIEIARIRDEIRKQIGVRYDED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17251.t1 Gene3D G3DSA:3.40.50.720 - 4 124 0.0e+00
8 g17251.t1 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 125 335 0.0e+00
3 g17251.t1 PANTHER PTHR22604 OXIDOREDUCTASES 2 334 0.0e+00
4 g17251.t1 PANTHER PTHR22604:SF105 TRANS-1,2-DIHYDROBENZENE-1,2-DIOL DEHYDROGENASE 2 334 0.0e+00
1 g17251.t1 Pfam PF01408 Oxidoreductase family, NAD-binding Rossmann fold 5 123 0.0e+00
2 g17251.t1 Pfam PF02894 Oxidoreductase family, C-terminal alpha/beta domain 138 254 3.3e-05
5 g17251.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 156 0.0e+00
6 g17251.t1 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 131 300 0.0e+00

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:0016491 oxidoreductase 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