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 g6775 g6775.t2 TSS g6775.t2 18562263 18562263
chr_2 g6775 g6775.t2 isoform g6775.t2 18562371 18563461
chr_2 g6775 g6775.t2 exon g6775.t2.exon1 18562371 18562444
chr_2 g6775 g6775.t2 cds g6775.t2.CDS1 18562371 18562444
chr_2 g6775 g6775.t2 exon g6775.t2.exon2 18562521 18562784
chr_2 g6775 g6775.t2 cds g6775.t2.CDS2 18562521 18562784
chr_2 g6775 g6775.t2 exon g6775.t2.exon3 18562840 18563461
chr_2 g6775 g6775.t2 cds g6775.t2.CDS3 18562840 18563461
chr_2 g6775 g6775.t2 TTS g6775.t2 18563567 18563567

Sequences

>g6775.t2 Gene=g6775 Length=960
ATGGACTGGTGGCTCATTCTATTAATTATAATTTTAGTGTTATTAGGAATTTTTGCTCTT
TTGTATTTATTAAAATTATACATTAGACGAGCAAGATTCACTAAAACTACTAGAATTACT
GATAAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGAAAAGAGACTGCCATTGAC
TTGGCAAAACGAGGTGGGAAAATTTATATTGTATGTCGCGATCAAAAACGCGGTGAGGAT
GCATTGAAAGAAATAAAAGAAAGAAGTGGCAGTGACAAAGTTCATTTCATGCAACTTGAT
CTGGCTTCTCTAGAATCTGTTCGTAAATTTTCACTAAGATTTCATGAATTGGAGCATCAA
TTGCACATTCTCATAAATAATGCAGGTGTAATGGCCTGTCCAAAATCATATACAGCTGAT
GGATATGAATTGCAATTTGGAACTAATCATTTAGGGCATTTTCTGCTCACAAATTTATTG
CTTGATTTGTTAAAAGCCGGCGCACCGAGTCGAATAGTAGTTGTGTCTAGTGCTGCATAT
CAAATCGGTAGAATAAATAAAGAAGATTTGATGTATGAAAAGAGTTACAATAAATACAAA
GCTTATGGGCAAAGTAAACTTGCAAACATTCTATTTACACGTGAATTAGCAAAACGACTT
GATGGCACAGGTGTCAATGTCAATAGCTGTCATCCTGGCGTTGTTCAAACTGAATTAGGA
AGATATATGGATGAAAATATTCGAAAGTATTTTATCAAACCTATTTTAGGTCCATTTTTT
AAAATTCCATATGAAGGAGCCCAAACTCAAATTCGATTAGCTGTTGATCCTGATTTAGAT
AAAGTGACAGGAAAATATTTTGCCGATTGCAAAGAACATTCACTAAGAAGTAATGCACAA
TGTGAAGAAATTGCAGAATGGCTGTGGAAAAAAAGTGCTGAATTTGTGGGACCTTGTTAA

>g6775.t2 Gene=g6775 Length=319
MDWWLILLIIILVLLGIFALLYLLKLYIRRARFTKTTRITDKIVIITGANTGIGKETAID
LAKRGGKIYIVCRDQKRGEDALKEIKERSGSDKVHFMQLDLASLESVRKFSLRFHELEHQ
LHILINNAGVMACPKSYTADGYELQFGTNHLGHFLLTNLLLDLLKAGAPSRIVVVSSAAY
QIGRINKEDLMYEKSYNKYKAYGQSKLANILFTRELAKRLDGTGVNVNSCHPGVVQTELG
RYMDENIRKYFIKPILGPFFKIPYEGAQTQIRLAVDPDLDKVTGKYFADCKEHSLRSNAQ
CEEIAEWLWKKSAEFVGPC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g6775.t2 Gene3D G3DSA:3.40.50.720 - 29 318 7.4E-88
2 g6775.t2 PANTHER PTHR24320 RETINOL DEHYDROGENASE 9 317 1.3E-133
3 g6775.t2 PANTHER PTHR24320:SF142 GH10714P-RELATED 9 317 1.3E-133
11 g6775.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 43 60 1.5E-17
6 g6775.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 119 130 5.6E-5
9 g6775.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 119 130 1.5E-17
8 g6775.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 164 180 1.5E-17
4 g6775.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 170 178 5.6E-5
5 g6775.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 202 221 5.6E-5
7 g6775.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 202 221 1.5E-17
10 g6775.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 223 240 1.5E-17
1 g6775.t2 Pfam PF00106 short chain dehydrogenase 42 245 2.3E-35
16 g6775.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
17 g6775.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 28 -
15 g6775.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 29 319 -
13 g6775.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 40 294 1.37E-60
12 g6775.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 26 -

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

Pathway

  • This transcript belongs to the following pathways

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