Gene loci information

Transcript annotation

  • This transcript has been annotated as Retinol dehydrogenase 12.

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_2 g6779 g6779.t1 TSS g6779.t1 18571442 18571442
chr_2 g6779 g6779.t1 isoform g6779.t1 18571497 18572612
chr_2 g6779 g6779.t1 exon g6779.t1.exon1 18571497 18571519
chr_2 g6779 g6779.t1 cds g6779.t1.CDS1 18571497 18571519
chr_2 g6779 g6779.t1 exon g6779.t1.exon2 18571573 18571643
chr_2 g6779 g6779.t1 cds g6779.t1.CDS2 18571573 18571643
chr_2 g6779 g6779.t1 exon g6779.t1.exon3 18571702 18572256
chr_2 g6779 g6779.t1 cds g6779.t1.CDS3 18571702 18572256
chr_2 g6779 g6779.t1 exon g6779.t1.exon4 18572320 18572612
chr_2 g6779 g6779.t1 cds g6779.t1.CDS4 18572320 18572612
chr_2 g6779 g6779.t1 TTS g6779.t1 NA NA

Sequences

>g6779.t1 Gene=g6779 Length=942
ATGAAAACCTTTTTAAAAAGCTTCTTAAATATCGTCAATAAACCTATTTATAAGAAAAAT
ACAAAAATCGATAATAAAGTCGTTATAATAACAGGAGGAAATTCAGGAATCGGAAAAGAA
ACAGCAGTTGATTTAGCAAAACGTGGTGGAAAAATCTACATTGCTTGTAGAGATGTTATT
CGTAGTCAACAAGATCTTGAAGAGATCAAAGGAAGAGCCAAAGCTTCGAAAGTCTATCTT
ATGGAACTTGACCTTGCTTCAATAAAATCAATCAGAAAATTTTCAAGAGAATTTCATGAA
CGAGAAAAAAAATTACATATTCTCATAAATAATGCAGGTGTAATGGCTTGCCCAAAATCA
TATACAAAAGATGGATTTGAAATGCAAATGGGAGTTAATCATTTAGGTCATTTCTTGCTA
ACAAATCTGCTTCTTGATATGCTTAAATTATCTGCACCAAGTCGAATCGTCGTTGTATCT
TCTTCAGGCCACAAGCTTTCTGGAATAAATCGAGATGATTTTATGAGTGAAAAGAGTTAT
AATAAAATAAAAGCTTATGGTCAAAGTAAATTAGCAAACATTTTATTTGCTCTGGAATTA
TCGAGAAGACTTCATGGTTTAGATGTAACTTGTAACTCGCTACATCCTGGACTTGTACAT
ACAAATCTTGGAAGACATATGAACTCGCGCTTTCGTCCAATTTATGGAAAAGTTTTGAAA
CCATTTTACAAAACTACATTTGAAGGAGCTCAAACACAAATTCGGTTAGCAGTTGATCCT
GATTTAGAAGGTGTAACAGGAAAATATTTTGTTGATTGTGAAGAAGCAACACCATCAGAA
GAAGCTCAAAGTTATGAAACAGCAGCATGGTTATGGAACAAAAGTACTCAATTAATTTAT
GATAAATTTAAGAAATTTGATTTAGACAATAAAAATAATTAA

>g6779.t1 Gene=g6779 Length=313
MKTFLKSFLNIVNKPIYKKNTKIDNKVVIITGGNSGIGKETAVDLAKRGGKIYIACRDVI
RSQQDLEEIKGRAKASKVYLMELDLASIKSIRKFSREFHEREKKLHILINNAGVMACPKS
YTKDGFEMQMGVNHLGHFLLTNLLLDMLKLSAPSRIVVVSSSGHKLSGINRDDFMSEKSY
NKIKAYGQSKLANILFALELSRRLHGLDVTCNSLHPGLVHTNLGRHMNSRFRPIYGKVLK
PFYKTTFEGAQTQIRLAVDPDLEGVTGKYFVDCEEATPSEEAQSYETAAWLWNKSTQLIY
DKFKKFDLDNKNN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6779.t1 Gene3D G3DSA:3.40.50.720 - 16 305 0
2 g6779.t1 PANTHER PTHR24320 RETINOL DEHYDROGENASE 13 299 0
3 g6779.t1 PANTHER PTHR24320:SF142 GH10714P-RELATED 13 299 0
6 g6779.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 27 44 0
5 g6779.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 103 114 0
4 g6779.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 207 224 0
1 g6779.t1 Pfam PF00106 short chain dehydrogenase 26 228 0
7 g6779.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 24 276 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

## [1] "No matching GO terms"

KEGG

Orthology

Pathway

This gene does not belong to any 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