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 g15457 g15457.t2 isoform g15457.t2 5519414 5521775
chr_4 g15457 g15457.t2 exon g15457.t2.exon1 5519414 5519436
chr_4 g15457 g15457.t2 exon g15457.t2.exon2 5519782 5520098
chr_4 g15457 g15457.t2 cds g15457.t2.CDS1 5519841 5520098
chr_4 g15457 g15457.t2 exon g15457.t2.exon3 5520159 5520405
chr_4 g15457 g15457.t2 cds g15457.t2.CDS2 5520159 5520405
chr_4 g15457 g15457.t2 exon g15457.t2.exon4 5520464 5520755
chr_4 g15457 g15457.t2 cds g15457.t2.CDS3 5520464 5520755
chr_4 g15457 g15457.t2 exon g15457.t2.exon5 5521571 5521775
chr_4 g15457 g15457.t2 cds g15457.t2.CDS4 5521571 5521775
chr_4 g15457 g15457.t2 TSS g15457.t2 5521865 5521865
chr_4 g15457 g15457.t2 TTS g15457.t2 NA NA

Sequences

>g15457.t2 Gene=g15457 Length=1084
ATGGCACCATTACGTTGGGGAATTGCATCAGCTGGTAAAATTTCAAATGACTTTTGTGCA
GCTTTATCAACATATTCTCAAGATGATCATCAGGTCGTCGCGGTTGCGGCTCGCTCATTG
GAGGATGCAAAGGAATTTGCAGAAACATTCAATATTCCTAGGACTCATGAAGGTTACCAA
AAATTAGCTCAGGATCCAGAAGTTGATGTTGTTTATATTGGATCTATTAATACCACACAT
CTTGAAATTGGTTTAATGATGTTGGATGGTGGCAAACATATTCTTTGTGAAAAGCCTTTG
ACATTAAATGTAAAACAAGCTGAACAACTTTTAAATCATGCAAAAGAGAAGAAATTATTT
TGTATGGAAGCAATTTGGTCAAGATATTTTCCAATTTATAGACAACTTAAAGCTCGTATT
AACAATGGTGATCTTGGTGACATTAAAGAAGTTTATGCTGAATTTGGTGTTGAAATGGCA
GATGTTGATCGTGTAATGAAAAATGAACTTGGAGGTGGTTCCACATTGGATATTGGAACC
TATGCAATTCAATTTTCTCAATTTGTCTTTCGTGCTGAACCGACATCAATTAAAGCAACT
GGCAAATTAAATGAAGAAGGTGTTGATACTGAAACTGAAGTTGAATTAAAATATCCAAAT
GGTGGTGTTGCTCGTTATAAGACTAATTCAACAAAAGAACTCAGCAACATTGCAACTGTA
ACAGGAAGCAAAGGCACAATGAAGCTCCATACTTTCTGGTGTCCAACTGAATTAGAAGAT
GTTGATGGTCAAATGAAAAAATTCGAATTACCACAAAATCGACTTGGTAAATTTATTTAC
TTCCATGGTGCTGGCATGCGATATGAAGCAGAAGAAGTAAGAAGATGCATCAATGAAGGT
TTGACTGAAAGTGAAGATGCAACACATAATGACAGTCTTGTCATTGCTCGTATTCGTGAT
GAAATTCGTAGACAACTTGGTGTTAAATTTGATGAAGACTGAAATTTAATGGAAACTAAA
TTATGAAATGGATCTCTTGAAATGTGACATGATAAGCAAAGAGTTCTCAGGCCTTGATTT
TACA

>g15457.t2 Gene=g15457 Length=333
MAPLRWGIASAGKISNDFCAALSTYSQDDHQVVAVAARSLEDAKEFAETFNIPRTHEGYQ
KLAQDPEVDVVYIGSINTTHLEIGLMMLDGGKHILCEKPLTLNVKQAEQLLNHAKEKKLF
CMEAIWSRYFPIYRQLKARINNGDLGDIKEVYAEFGVEMADVDRVMKNELGGGSTLDIGT
YAIQFSQFVFRAEPTSIKATGKLNEEGVDTETEVELKYPNGGVARYKTNSTKELSNIATV
TGSKGTMKLHTFWCPTELEDVDGQMKKFELPQNRLGKFIYFHGAGMRYEAEEVRRCINEG
LTESEDATHNDSLVIARIRDEIRRQLGVKFDED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g15457.t2 Gene3D G3DSA:3.40.50.720 - 3 123 0
8 g15457.t2 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 124 333 0
3 g15457.t2 PANTHER PTHR22604 OXIDOREDUCTASES 2 331 0
4 g15457.t2 PANTHER PTHR22604:SF105 TRANS-1,2-DIHYDROBENZENE-1,2-DIOL DEHYDROGENASE 2 331 0
1 g15457.t2 Pfam PF01408 Oxidoreductase family, NAD-binding Rossmann fold 4 121 0
2 g15457.t2 Pfam PF02894 Oxidoreductase family, C-terminal alpha/beta domain 137 296 0
5 g15457.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 156 0
6 g15457.t2 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 130 298 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: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