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.t7 TSS g6774.t7 18559579 18559579
chr_2 g6774 g6774.t7 isoform g6774.t7 18559627 18561525
chr_2 g6774 g6774.t7 exon g6774.t7.exon1 18559627 18559697
chr_2 g6774 g6774.t7 cds g6774.t7.CDS1 18559627 18559697
chr_2 g6774 g6774.t7 exon g6774.t7.exon2 18559758 18560021
chr_2 g6774 g6774.t7 cds g6774.t7.CDS2 18559758 18560021
chr_2 g6774 g6774.t7 exon g6774.t7.exon3 18561403 18561525
chr_2 g6774 g6774.t7 cds g6774.t7.CDS3 18561403 18561427
chr_2 g6774 g6774.t7 TTS g6774.t7 18562130 18562130

Sequences

>g6774.t7 Gene=g6774 Length=458
ATGGAAAACTGTTTTTGTGGAAATAAACTTTTAATTTTAATTGGAGTAGCAAGTTTAATC
TATTTTCTAAAAACATATATTCGTCGAGCAAAATTTACTAAAACTACTAGAATCGATGGA
AAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGAAAAGAGACTGCCATTGACTTG
GCTAAACGTGGTGGAAAAATTTATATTGCATGTCGCGATGAAAAACGCGGTGAGGATGCA
TTGAAAGAAATAAAAGAAAGAAGTGACAGTGACAAAGTTCATTTCATGCAACTTGATCTG
GCTTCTCTAGAATCTGTTCGTAAATTTTCACAAAGAGAGAAAATCAGTTACATATATTGA
TAAATAATGCAGGAGTAATGGCTTGTCCAAGAATGGAAACTAAAGATGGATTTGAATTAC
AAATTGGAACAAATCATCTTGGACATTTTTTACTTACA

>g6774.t7 Gene=g6774 Length=119
MENCFCGNKLLILIGVASLIYFLKTYIRRAKFTKTTRIDGKIVIITGANTGIGKETAIDL
AKRGGKIYIACRDEKRGEDALKEIKERSDSDKVHFMQLDLASLESVRKFSQREKISYIY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g6774.t7 Gene3D G3DSA:3.40.50.720 - 24 115 1.7E-24
2 g6774.t7 PANTHER PTHR24320 RETINOL DEHYDROGENASE 8 112 2.4E-32
3 g6774.t7 PANTHER PTHR24320:SF142 GH10714P-RELATED 8 112 2.4E-32
1 g6774.t7 Pfam PF00106 short chain dehydrogenase 41 111 6.6E-14
8 g6774.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
9 g6774.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 27 -
7 g6774.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 28 119 -
5 g6774.t7 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 25 111 4.89E-20
4 g6774.t7 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. There were no conditions that were differentially expressed