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 g7125 g7125.t8 TSS g7125.t8 21356696 21356696
chr_2 g7125 g7125.t8 isoform g7125.t8 21356774 21357907
chr_2 g7125 g7125.t8 exon g7125.t8.exon1 21356774 21356853
chr_2 g7125 g7125.t8 cds g7125.t8.CDS1 21356774 21356853
chr_2 g7125 g7125.t8 exon g7125.t8.exon2 21356952 21357410
chr_2 g7125 g7125.t8 cds g7125.t8.CDS2 21356952 21357410
chr_2 g7125 g7125.t8 exon g7125.t8.exon3 21357469 21357635
chr_2 g7125 g7125.t8 cds g7125.t8.CDS3 21357469 21357635
chr_2 g7125 g7125.t8 exon g7125.t8.exon4 21357738 21357907
chr_2 g7125 g7125.t8 cds g7125.t8.CDS4 21357738 21357907
chr_2 g7125 g7125.t8 TTS g7125.t8 21357983 21357983

Sequences

>g7125.t8 Gene=g7125 Length=876
ATGTTCTCAATATTAAAGAAAAAAAGTATTGTATGGAGCTCGACTATTATTGCTGGTTTG
GGCATTACATTTATCATTAAAGATTCAGTACAAGGAGAACGATTTAAAAAATCTATTGTT
GTAGATGGAAAAGTATTTATTGTTACTGGAGCTAACACAGGAATAGGCAAAGAAACTGCA
AAAAATCTTGCGAAAAGAAGAGGAATTGTTTATTTAGCATGTAGAGATTTACACAAATGC
GAAGCAGCAAGAAAAGAGATAATTCTGGCTACAAGAAATAAAAATGTCTTTTGTCGTGAA
CTTGATTTAGCTTCATTTAGTTCAATTAGAAGTTTTGTAAAGAGATTTAAATCAGAGCAA
AATCGTTTGGATGTTTTAATTAATAACGCAGGCGTTATGAGAATCCCACAAAAGCTTGTT
ACCCAAGAAGGATTCGAAATGCAGATTGGTACAAATCATTTAGGCCATTTTTTACTTACA
AATTTGTTATTAGATTATCTTAAAGCCTCTGCTCCTTCGCGAATTGTAACTGTATCAAGT
ATTGCTCATACACGTGGTGAAATAGATACAGCAGATTTCAATAGTGACAAAAATTATGAT
CCTAAGAAAGCTTATGAAATGTCAAAATTATGCAACGTACTCTTCACAAGACAGCTTGCA
AAAAAATTAGAAGGGACGGGAGTTACTTCGAACTGCTGTCATCCTGAAGCTGGTGCTCAA
ACTGTTTTGTTTTGTGTACTTGAACCTGCGTTAAAAAATATTACTGGCGAATATTTCGCA
GATTGTAAAAAGTCTGAAATGGCAGACCAAGCGAAAGATGATCAAATGGCAGAATGGTTG
TGGCGCTTAAGTGAAAAATGGTGCCGATTAGCTTGA

>g7125.t8 Gene=g7125 Length=291
MFSILKKKSIVWSSTIIAGLGITFIIKDSVQGERFKKSIVVDGKVFIVTGANTGIGKETA
KNLAKRRGIVYLACRDLHKCEAARKEIILATRNKNVFCRELDLASFSSIRSFVKRFKSEQ
NRLDVLINNAGVMRIPQKLVTQEGFEMQIGTNHLGHFLLTNLLLDYLKASAPSRIVTVSS
IAHTRGEIDTADFNSDKNYDPKKAYEMSKLCNVLFTRQLAKKLEGTGVTSNCCHPEAGAQ
TVLFCVLEPALKNITGEYFADCKKSEMADQAKDDQMAEWLWRLSEKWCRLA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g7125.t8 Gene3D G3DSA:3.40.50.720 - 36 290 2.6E-75
3 g7125.t8 PANTHER PTHR24320 RETINOL DEHYDROGENASE 12 235 2.8E-120
5 g7125.t8 PANTHER PTHR24320:SF142 GH10714P-RELATED 12 235 2.8E-120
2 g7125.t8 PANTHER PTHR24320 RETINOL DEHYDROGENASE 235 289 2.8E-120
4 g7125.t8 PANTHER PTHR24320:SF142 GH10714P-RELATED 235 289 2.8E-120
10 g7125.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 45 62 3.5E-14
7 g7125.t8 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 121 132 4.3E-7
9 g7125.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 121 132 3.5E-14
12 g7125.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 167 183 3.5E-14
6 g7125.t8 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 173 181 4.3E-7
8 g7125.t8 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 205 224 4.3E-7
11 g7125.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 205 224 3.5E-14
1 g7125.t8 Pfam PF00106 short chain dehydrogenase 44 236 2.5E-28
16 g7125.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 8 -
18 g7125.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
17 g7125.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 291 -
14 g7125.t8 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 42 265 4.71E-52
13 g7125.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 9 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

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