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 g6774 g6774.t14 TSS g6774.t14 18559579 18559579
chr_2 g6774 g6774.t14 isoform g6774.t14 18559627 18562076
chr_2 g6774 g6774.t14 exon g6774.t14.exon1 18559627 18559697
chr_2 g6774 g6774.t14 cds g6774.t14.CDS1 18559627 18559697
chr_2 g6774 g6774.t14 exon g6774.t14.exon2 18559758 18560021
chr_2 g6774 g6774.t14 cds g6774.t14.CDS2 18559758 18560021
chr_2 g6774 g6774.t14 exon g6774.t14.exon3 18561393 18561754
chr_2 g6774 g6774.t14 cds g6774.t14.CDS3 18561393 18561754
chr_2 g6774 g6774.t14 exon g6774.t14.exon4 18561813 18562076
chr_2 g6774 g6774.t14 cds g6774.t14.CDS4 18561813 18561826
chr_2 g6774 g6774.t14 TTS g6774.t14 18562130 18562130

Sequences

>g6774.t14 Gene=g6774 Length=961
ATGGAAAACTGTTTTTGTGGAAATAAACTTTTAATTTTAATTGGAGTAGCAAGTTTAATC
TATTTTCTAAAAACATATATTCGTCGAGCAAAATTTACTAAAACTACTAGAATCGATGGA
AAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGAAAAGAGACTGCCATTGACTTG
GCTAAACGTGGTGGAAAAATTTATATTGCATGTCGCGATGAAAAACGCGGTGAGGATGCA
TTGAAAGAAATAAAAGAAAGAAGTGACAGTGACAAAGTTCATTTCATGCAACTTGATCTG
GCTTCTCTAGAATCTGTTCGTAAATTTTCACAAAGATTTCATGAGAGAGAAAATCAGTTA
CATATATTGATAAATAATGCAGGAGTAATGGCTTGTCCAAGAATGGAAACTAAAGATGGA
TTTGAATTACAAATTGGAACAAATCATCTTGGACATTTTTTACTTACACATCTATTACTC
GATCTTTTAAAATCAGTGTCTTCATCTCGAATTATTAATGTTTCGTCAGCAGCTCACAAG
TTTGGTGGTGTAAGCAAAAAAGATTTTATGAGTCAAAAAAATTATAATAGATGGTTCGCA
TATGGACAAAGCAAATTGGCGAATATTTTGTTCACACGTGAATTGGCAAAACGACTAAAA
GATTATCCGAATTTAACTGTCAACTCCTGCCACCCTGATAGGTGCTGTTAATACAGAACT
TCAAAGACATATGAATAAATTTCTTTGGGAGTATACATTATTACCAATTCTTGGAATATT
TTTTAAAACTCCATATGAAGGAGCTCAAACCCAAATTAAGTTGGCCGTTGATCCTGATTT
AGAAGGTGTAACAGGAAAATATTTTGTTGATTGCAAAGAAGCCAAAACATCAAAAGCAGC
TCAAAATGATGATGATGCCGAATGGCTTTATAAAAAAAGTATTGAATTAGTAGGACTGTA
A

>g6774.t14 Gene=g6774 Length=236
MENCFCGNKLLILIGVASLIYFLKTYIRRAKFTKTTRIDGKIVIITGANTGIGKETAIDL
AKRGGKIYIACRDEKRGEDALKEIKERSDSDKVHFMQLDLASLESVRKFSQRFHERENQL
HILINNAGVMACPRMETKDGFELQIGTNHLGHFLLTHLLLDLLKSVSSSRIINVSSAAHK
FGGVSKKDFMSQKNYNRWFAYGQSKLANILFTRELAKRLKDYPNLTVNSCHPDRCC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g6774.t14 Gene3D G3DSA:3.40.50.720 - 27 235 3.7E-70
2 g6774.t14 PANTHER PTHR24320 RETINOL DEHYDROGENASE 8 232 2.5E-98
3 g6774.t14 PANTHER PTHR24320:SF142 GH10714P-RELATED 8 232 2.5E-98
10 g6774.t14 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 42 59 2.1E-15
4 g6774.t14 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 118 129 1.4E-7
7 g6774.t14 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 118 129 2.1E-15
11 g6774.t14 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 163 179 2.1E-15
6 g6774.t14 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 169 177 1.4E-7
5 g6774.t14 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 201 220 1.4E-7
8 g6774.t14 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 201 220 2.1E-15
9 g6774.t14 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 223 236 2.1E-15
1 g6774.t14 Pfam PF00106 short chain dehydrogenase 41 232 1.3E-33
16 g6774.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
17 g6774.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 27 -
15 g6774.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 28 236 -
13 g6774.t14 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 39 232 1.83E-51
12 g6774.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 27 -

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.

Raw TPM values