Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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 g6776 g6776.t3 TSS g6776.t3 18563759 18563759
chr_2 g6776 g6776.t3 isoform g6776.t3 18563913 18564968
chr_2 g6776 g6776.t3 exon g6776.t3.exon1 18563913 18564968
chr_2 g6776 g6776.t3 cds g6776.t3.CDS1 18564081 18564968
chr_2 g6776 g6776.t3 TTS g6776.t3 18565061 18565061

Sequences

>g6776.t3 Gene=g6776 Length=1056
ATGGATGATGATAATAAAGAAACTCCATTGTGGCTAAAAGCCGTATATTATATTCTTCCA
ATATTTGGCACATCAGGACTACTTTATTTATTTAGGTACTTAAGTTGAAAGTTTTTTAAA
GTTACCTAAAAATTCTTTAAAATTTTAAAACAATGTATTAGATACTTCATGAAGAGTGAC
ATGTATAAGAAAGAAACTAAAATTGGTGGAAAAGTCGTTCTTATAACTGGAATTAACTCT
GATATTGGAATTTCAACTGCAATTAATTTGGCAAAACGTGACGGTAAAATCTATATTGCA
TGTGATGACAGTACTCGTGGTGAGGAAGTATTGAAAGAAATTAAAAAAAAATCAAAACGT
GACAACATTCACTTTATGAATCTTAATCTGGGATCATTAGAATCTATCCGACAGTTTTCT
AAAAAATTTCATGAAATGGAAAAAAAGTTAGACATTTTAATTAACAATCATGAATTGGTG
GCAAAAGAAAAATCTAAAACTGTTGAGGGATATGAACTCCATATGGGTGTAAACTATTTG
GGACATTTTTATCTTACACATCTTTTGCTTGATTTACTTAAAAGTGCAGCTCCTAGTAGA
ATTATTTTTGAAAGCTCTCTTGCTTATAAATGGGGTACAATTAACAAGGAAGATTTTATG
AGTGATAATTCGTATAATCGATTCAAAGCATATTGTAATAGCAAACTGGCTATTCATCTT
CTTGTACATGAATTGGCAAAAGAATTATCTGGTAGCTTGTGCACAGTGAATATAGCAATG
CCTGGTTTTGTTATAAGTGATATTGTAAGAAGAATTACTGGATTTTCTAAAGTGCAAAAA
GTTTTGGAATGGATGGGAGCAAAATTTATTAACACAGGCAAGGAAGGTGCACAAACAGTA
ATATTTACAGCAGTTGATACTGATATAAGTACTATTTCCGGAAAATGTTATGTTAATTGC
AAGGAAATTCAACCATCTAGTAAGTCAACTGAAGATGAAACATCCACATGGTTGTGGAAG
AAGGGAGAAGAGATATTGGGTATAAATTACGTTTAG

>g6776.t3 Gene=g6776 Length=295
MKSDMYKKETKIGGKVVLITGINSDIGISTAINLAKRDGKIYIACDDSTRGEEVLKEIKK
KSKRDNIHFMNLNLGSLESIRQFSKKFHEMEKKLDILINNHELVAKEKSKTVEGYELHMG
VNYLGHFYLTHLLLDLLKSAAPSRIIFESSLAYKWGTINKEDFMSDNSYNRFKAYCNSKL
AIHLLVHELAKELSGSLCTVNIAMPGFVISDIVRRITGFSKVQKVLEWMGAKFINTGKEG
AQTVIFTAVDTDISTISGKCYVNCKEIQPSSKSTEDETSTWLWKKGEEILGINYV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g6776.t3 Coils Coil Coil 80 100 -
10 g6776.t3 Gene3D G3DSA:3.40.50.720 - 6 295 2.9E-62
2 g6776.t3 PANTHER PTHR24320 RETINOL DEHYDROGENASE 4 291 6.2E-89
3 g6776.t3 PANTHER PTHR24320:SF142 GH10714P-RELATED 4 291 6.2E-89
7 g6776.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 16 33 5.9E-10
6 g6776.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 92 103 5.9E-10
5 g6776.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 175 194 5.9E-10
4 g6776.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 196 213 5.9E-10
1 g6776.t3 Pfam PF00106 short chain dehydrogenase 15 215 3.2E-25
9 g6776.t3 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 162 190 -
8 g6776.t3 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 14 267 1.66E-44

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:0055114 NA NA
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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