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 g6778 g6778.t2 TTS g6778.t2 18569792 18569792
chr_2 g6778 g6778.t2 isoform g6778.t2 18569895 18571045
chr_2 g6778 g6778.t2 exon g6778.t2.exon1 18569895 18570102
chr_2 g6778 g6778.t2 cds g6778.t2.CDS1 18569895 18570102
chr_2 g6778 g6778.t2 exon g6778.t2.exon2 18570163 18570208
chr_2 g6778 g6778.t2 cds g6778.t2.CDS2 18570163 18570208
chr_2 g6778 g6778.t2 exon g6778.t2.exon3 18570264 18570886
chr_2 g6778 g6778.t2 cds g6778.t2.CDS3 18570264 18570886
chr_2 g6778 g6778.t2 exon g6778.t2.exon4 18570951 18571045
chr_2 g6778 g6778.t2 cds g6778.t2.CDS4 18570951 18571045
chr_2 g6778 g6778.t2 TSS g6778.t2 18571007 18571007

Sequences

>g6778.t2 Gene=g6778 Length=972
ATGGAGTTTTTTAAAAATCTCAACTCCACATTAACTTTAGTCATCATTGTAACTTCTGCT
TTAATATTTGTTTGCGTTGTTTTATTGCTGTTCAGAATGTGGATGCAAGGAGGTCAATTT
AGAAAAGACACTAGAATCGATGGAAAAATTGTAATCATCACCGGTGCAAATGCAGGCATC
GGAAAAGAGACTGCCATTGACTTGGCAAAACGTGGTGGAAAAATTTATATTGCATGTCGC
GATGAAAAACGCGGTGAAAATGCTCAAATGGAAATTATTGAAAAAAGTGGCAGTGACAAA
GTTCATTTCATGCAACTTGATTTAGCTTCATTACAATCTGTTCGAGAATTTGTACAAAAA
TTTCATCAAGTTGAGAGTAAATTGCATATTCTGATAAATAATGCAGGTGTAATGGCTTGT
CCAAAATCATATACAGCTGATGGATATGAATTGCAATTTGGAACTAATCATTTGGGGCAT
TTTTTACTCACAAATTTATTACTTGATTTGTTAAAAGCCGGCGCACCAAGTCGAATTATT
AATGTCTCAAGTATTTTACATAACATAGGCAGAATAAACAAGCAAGATTTGATGCATCAA
GAAAGTTATTGGAAGTGGCTTGTTTATGGACAAAGTAAACTTGCAAACATTTTGTTTACA
CGTGAATTGGCAAAACAACTCGATGGCACTGGTGTTACAGTGAACTCACTTCATCCAGGA
GCTGTTAACACGGAATTATCACGAAACTTAGATTTATGCTCTAAATTCATTTTTCATCCT
GTAAAATGGTTGGTCTTCAAAACACCCAAATCTGGAGCTCAAACTCAAATTTATTTGGCC
GTTGACCCCGAACTTGAAAATGTAACAGGAAAGTATTTTGCTGATTGCAAAGAAAAAAGT
CCTTCAAGTGCGGCACGTGATGACGAAACCGCGCGTTGGTTATGGAAAGAAAGTGAAAAA
CTTACCAACATG

>g6778.t2 Gene=g6778 Length=324
MEFFKNLNSTLTLVIIVTSALIFVCVVLLLFRMWMQGGQFRKDTRIDGKIVIITGANAGI
GKETAIDLAKRGGKIYIACRDEKRGENAQMEIIEKSGSDKVHFMQLDLASLQSVREFVQK
FHQVESKLHILINNAGVMACPKSYTADGYELQFGTNHLGHFLLTNLLLDLLKAGAPSRII
NVSSILHNIGRINKQDLMHQESYWKWLVYGQSKLANILFTRELAKQLDGTGVTVNSLHPG
AVNTELSRNLDLCSKFIFHPVKWLVFKTPKSGAQTQIYLAVDPELENVTGKYFADCKEKS
PSSAARDDETARWLWKESEKLTNM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g6778.t2 Gene3D G3DSA:3.40.50.720 - 40 324 7.5E-91
2 g6778.t2 PANTHER PTHR24320 RETINOL DEHYDROGENASE 16 323 2.0E-143
3 g6778.t2 PANTHER PTHR24320:SF142 GH10714P-RELATED 16 323 2.0E-143
10 g6778.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 50 67 4.1E-21
6 g6778.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 126 137 5.3E-8
11 g6778.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 126 137 4.1E-21
8 g6778.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 171 187 4.1E-21
5 g6778.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 177 185 5.3E-8
4 g6778.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 209 228 5.3E-8
9 g6778.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 209 228 4.1E-21
7 g6778.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 230 247 4.1E-21
1 g6778.t2 Pfam PF00106 short chain dehydrogenase 49 250 4.7E-36
16 g6778.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
17 g6778.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 31 -
15 g6778.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 32 324 -
13 g6778.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 47 298 1.85E-63
12 g6778.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -

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

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