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.t4 TSS g6776.t4 18563759 18563759
chr_2 g6776 g6776.t4 isoform g6776.t4 18563913 18567386
chr_2 g6776 g6776.t4 exon g6776.t4.exon1 18563913 18564007
chr_2 g6776 g6776.t4 cds g6776.t4.CDS1 18563913 18564007
chr_2 g6776 g6776.t4 exon g6776.t4.exon2 18564074 18565047
chr_2 g6776 g6776.t4 cds g6776.t4.CDS2 18564074 18564968
chr_2 g6776 g6776.t4 TTS g6776.t4 18565061 18565061
chr_2 g6776 g6776.t4 exon g6776.t4.exon3 18567358 18567386

Sequences

>g6776.t4 Gene=g6776 Length=1098
ATGGATGATGATAATAAAGAAACTCCATTGTGGCTAAAAGCCGTATATTATATTCTTCCA
ATATTTGGCACATCAGGACTACTTTATTTATTTAGATACTTCATGAAGAGTGACATGTAT
AAGAAAGAAACTAAAATTGGTGGAAAAGTCGTTCTTATAACTGGAATTAACTCTGATATT
GGAATTTCAACTGCAATTAATTTGGCAAAACGTGACGGTAAAATCTATATTGCATGTGAT
GACAGTACTCGTGGTGAGGAAGTATTGAAAGAAATTAAAAAAAAATCAAAACGTGACAAC
ATTCACTTTATGAATCTTAATCTGGGATCATTAGAATCTATCCGACAGTTTTCTAAAAAA
TTTCATGAAATGGAAAAAAAGTTAGACATTTTAATTAACAATCATGAATTGGTGGCAAAA
GAAAAATCTAAAACTGTTGAGGGATATGAACTCCATATGGGTGTAAACTATTTGGGACAT
TTTTATCTTACACATCTTTTGCTTGATTTACTTAAAAGTGCAGCTCCTAGTAGAATTATT
TTTGAAAGCTCTCTTGCTTATAAATGGGGTACAATTAACAAGGAAGATTTTATGAGTGAT
AATTCGTATAATCGATTCAAAGCATATTGTAATAGCAAACTGGCTATTCATCTTCTTGTA
CATGAATTGGCAAAAGAATTATCTGGTAGCTTGTGCACAGTGAATATAGCAATGCCTGGT
TTTGTTATAAGTGATATTGTAAGAAGAATTACTGGATTTTCTAAAGTGCAAAAAGTTTTG
GAATGGATGGGAGCAAAATTTATTAACACAGGCAAGGAAGGTGCACAAACAGTAATATTT
ACAGCAGTTGATACTGATATAAGTACTATTTCCGGAAAATGTTATGTTAATTGCAAGGAA
ATTCAACCATCTAGTAAGTCAACTGAAGATGAAACATCCACATGGTTGTGGAAGAAGGGA
GAAGAGATATTGGGTATAAATTACGTTTAGTTTATTTTCAAACTATATTATTTACTATTT
ACAAACACATTTTTTGTGTTCTCATTTCCATGACAACATAAAACAATAAAACTTTTAACG
TATTTTTAAAATAAAAAT

>g6776.t4 Gene=g6776 Length=329
MDDDNKETPLWLKAVYYILPIFGTSGLLYLFRYFMKSDMYKKETKIGGKVVLITGINSDI
GISTAINLAKRDGKIYIACDDSTRGEEVLKEIKKKSKRDNIHFMNLNLGSLESIRQFSKK
FHEMEKKLDILINNHELVAKEKSKTVEGYELHMGVNYLGHFYLTHLLLDLLKSAAPSRII
FESSLAYKWGTINKEDFMSDNSYNRFKAYCNSKLAIHLLVHELAKELSGSLCTVNIAMPG
FVISDIVRRITGFSKVQKVLEWMGAKFINTGKEGAQTVIFTAVDTDISTISGKCYVNCKE
IQPSSKSTEDETSTWLWKKGEEILGINYV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g6776.t4 Coils Coil Coil 114 134 -
9 g6776.t4 Gene3D G3DSA:3.40.50.720 - 39 329 4.1E-62
2 g6776.t4 PANTHER PTHR24320 RETINOL DEHYDROGENASE 24 325 2.4E-91
3 g6776.t4 PANTHER PTHR24320:SF142 GH10714P-RELATED 24 325 2.4E-91
6 g6776.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 50 67 8.4E-10
7 g6776.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 126 137 8.4E-10
5 g6776.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 209 228 8.4E-10
4 g6776.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 230 247 8.4E-10
1 g6776.t4 Pfam PF00106 short chain dehydrogenase 49 249 4.5E-25
12 g6776.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 13 -
13 g6776.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 14 35 -
11 g6776.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 36 329 -
16 g6776.t4 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 196 224 -
8 g6776.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 48 301 2.49E-44
15 g6776.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 34 -
14 g6776.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 46 68 -

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