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.t2 TSS g6776.t2 18563759 18563759
chr_2 g6776 g6776.t2 isoform g6776.t2 18563913 18564968
chr_2 g6776 g6776.t2 exon g6776.t2.exon1 18563913 18564007
chr_2 g6776 g6776.t2 cds g6776.t2.CDS1 18563913 18564007
chr_2 g6776 g6776.t2 exon g6776.t2.exon2 18564074 18564743
chr_2 g6776 g6776.t2 cds g6776.t2.CDS2 18564074 18564743
chr_2 g6776 g6776.t2 exon g6776.t2.exon3 18564893 18564968
chr_2 g6776 g6776.t2 cds g6776.t2.CDS3 18564893 18564895
chr_2 g6776 g6776.t2 TTS g6776.t2 18565061 18565061

Sequences

>g6776.t2 Gene=g6776 Length=841
ATGGATGATGATAATAAAGAAACTCCATTGTGGCTAAAAGCCGTATATTATATTCTTCCA
ATATTTGGCACATCAGGACTACTTTATTTATTTAGATACTTCATGAAGAGTGACATGTAT
AAGAAAGAAACTAAAATTGGTGGAAAAGTCGTTCTTATAACTGGAATTAACTCTGATATT
GGAATTTCAACTGCAATTAATTTGGCAAAACGTGACGGTAAAATCTATATTGCATGTGAT
GACAGTACTCGTGGTGAGGAAGTATTGAAAGAAATTAAAAAAAAATCAAAACGTGACAAC
ATTCACTTTATGAATCTTAATCTGGGATCATTAGAATCTATCCGACAGTTTTCTAAAAAA
TTTCATGAAATGGAAAAAAAGTTAGACATTTTAATTAACAATCATGAATTGGTGGCAAAA
GAAAAATCTAAAACTGTTGAGGGATATGAACTCCATATGGGTGTAAACTATTTGGGACAT
TTTTATCTTACACATCTTTTGCTTGATTTACTTAAAAGTGCAGCTCCTAGTAGAATTATT
TTTGAAAGCTCTCTTGCTTATAAATGGGGTACAATTAACAAGGAAGATTTTATGAGTGAT
AATTCGTATAATCGATTCAAAGCATATTGTAATAGCAAACTGGCTATTCATCTTCTTGTA
CATGAATTGGCAAAAGAATTATCTGGTAGCTTGTGCACAGTGAATATAGCAATGCCTGGT
TTTGTTATAAGTGATATTGTAAGAAGAATTACTGGATTTTCTAAATAAGTCAACTGAAGA
TGAAACATCCACATGGTTGTGGAAGAAGGGAGAAGAGATATTGGGTATAAATTACGTTTA
G

>g6776.t2 Gene=g6776 Length=255
MDDDNKETPLWLKAVYYILPIFGTSGLLYLFRYFMKSDMYKKETKIGGKVVLITGINSDI
GISTAINLAKRDGKIYIACDDSTRGEEVLKEIKKKSKRDNIHFMNLNLGSLESIRQFSKK
FHEMEKKLDILINNHELVAKEKSKTVEGYELHMGVNYLGHFYLTHLLLDLLKSAAPSRII
FESSLAYKWGTINKEDFMSDNSYNRFKAYCNSKLAIHLLVHELAKELSGSLCTVNIAMPG
FVISDIVRRITGFSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g6776.t2 Coils Coil Coil 114 134 -
9 g6776.t2 Gene3D G3DSA:3.40.50.720 - 39 254 3.0E-52
2 g6776.t2 PANTHER PTHR24320 RETINOL DEHYDROGENASE 24 251 2.1E-73
3 g6776.t2 PANTHER PTHR24320:SF142 GH10714P-RELATED 24 251 2.1E-73
6 g6776.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 50 67 3.7E-10
7 g6776.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 126 137 3.7E-10
5 g6776.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 209 228 3.7E-10
4 g6776.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 230 247 3.7E-10
1 g6776.t2 Pfam PF00106 short chain dehydrogenase 49 249 2.0E-25
12 g6776.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 13 -
13 g6776.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 14 35 -
11 g6776.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 36 255 -
15 g6776.t2 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 196 224 -
8 g6776.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 48 250 8.13E-41
14 g6776.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 34 -

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