General information for g881.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinol dehydrogenase 11.
Parent gene
- The parent gene g881 is located on chr_3: 6642868..6652920 (- strand)
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_3 | g881 | g881.t1 | isoform | g881.t1 | 6642868 | 6652920 |
| chr_3 | g881 | g881.t1 | exon | g881.t1.exon1 | 6642868 | 6642976 |
| chr_3 | g881 | g881.t1 | cds | g881.t1.CDS1 | 6642868 | 6642976 |
| chr_3 | g881 | g881.t1 | exon | g881.t1.exon2 | 6643085 | 6643127 |
| chr_3 | g881 | g881.t1 | cds | g881.t1.CDS2 | 6643085 | 6643127 |
| chr_3 | g881 | g881.t1 | exon | g881.t1.exon3 | 6643183 | 6643516 |
| chr_3 | g881 | g881.t1 | cds | g881.t1.CDS3 | 6643183 | 6643516 |
| chr_3 | g881 | g881.t1 | exon | g881.t1.exon4 | 6643669 | 6643770 |
| chr_3 | g881 | g881.t1 | cds | g881.t1.CDS4 | 6643669 | 6643770 |
| chr_3 | g881 | g881.t1 | exon | g881.t1.exon5 | 6644061 | 6644115 |
| chr_3 | g881 | g881.t1 | cds | g881.t1.CDS5 | 6644061 | 6644115 |
| chr_3 | g881 | g881.t1 | exon | g881.t1.exon6 | 6644189 | 6644335 |
| chr_3 | g881 | g881.t1 | cds | g881.t1.CDS6 | 6644189 | 6644335 |
| chr_3 | g881 | g881.t1 | exon | g881.t1.exon7 | 6644425 | 6644541 |
| chr_3 | g881 | g881.t1 | cds | g881.t1.CDS7 | 6644425 | 6644541 |
| chr_3 | g881 | g881.t1 | exon | g881.t1.exon8 | 6652895 | 6652920 |
| chr_3 | g881 | g881.t1 | cds | g881.t1.CDS8 | 6652895 | 6652920 |
| chr_3 | g881 | g881.t1 | TSS | g881.t1 | NA | NA |
| chr_3 | g881 | g881.t1 | TTS | g881.t1 | NA | NA |
Sequences
>g881.t1 Gene=g881 Length=933
ATGAGTTTCTTCAGTGATATTCAGGGAATTTTCATTCGTGGTGCGAGTTATAAGAAATCG
ACACGTTGCGATGGAAAAGTCGTTATCATAACGGGCGCAAATGCTGGCATAGGAAAAGAA
ACTGCTGTCGAATTAGCGGCACGGGGAGCGAAGGTGTACATTGCGTGCAGATCGATAGAG
AGGGGCCAAAGTGCTTGCAAAGAAATTATTCAGAGAACTGGCAATGAAAATGTATTTGTG
AGAAAATTAGATCTGGCCTCATTTGCTTCTATAAGGGAATTTGCTAAAGGGTTTTTAAAA
GAGGAAAAACAATTTGATATTCTTATTAATAATCCTGGCGTTATGGCAATTCCCCTGTGG
CGAACAGAAGACTTGCTTGAAATGCAAATTGGCGTGAATCACTTCGGACATTTTTTGCTC
ACAAATCTGCTACTGCCGTTGATTAAGGCGACTGAGTCAAGCCGAATTATAAATGTATCA
AGTATGGCACATCGTTGGGGAAAAATTAAGACAGACGATTTAAATAGTGAAAAATCATAC
AATGAAATTTCTTGTTATGCTCAAAGTAAATTGGCAAATATTCTTTTTACTCGTGAACTA
GCAAAAAGATTAAAAGACACAAAAACGACAGTAAATGCACTTCATCCTGGAGTTGTTAAA
ACAGAACTTGCAAGACATGTTGAAAAAATGAATTTTTTATTTAATTCAAAAATTTTAAGT
TTTTTCATGTATTTTTTTAATAAAACAGCAAAGCAAGGAGCTCAAACAACAATTTATGCA
GCCCTTGATCCTGATCTTGCAAACGTGAGCGGACAGTACTTTGCTGAATGCGGCCTTGGG
AAAATATACAAACAGGGCTTAGATGATGACATAGCAAAGTGGTTGTGGAATGTAAGTGAA
AAATGGACGAAACTCGACTCGAAATCTGAGTAG
>g881.t1 Gene=g881 Length=310
MSFFSDIQGIFIRGASYKKSTRCDGKVVIITGANAGIGKETAVELAARGAKVYIACRSIE
RGQSACKEIIQRTGNENVFVRKLDLASFASIREFAKGFLKEEKQFDILINNPGVMAIPLW
RTEDLLEMQIGVNHFGHFLLTNLLLPLIKATESSRIINVSSMAHRWGKIKTDDLNSEKSY
NEISCYAQSKLANILFTRELAKRLKDTKTTVNALHPGVVKTELARHVEKMNFLFNSKILS
FFMYFFNKTAKQGAQTTIYAALDPDLANVSGQYFAECGLGKIYKQGLDDDIAKWLWNVSE
KWTKLDSKSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g881.t1 | Gene3D | G3DSA:3.40.50.720 | - | 14 | 307 | 0e+00 |
| 2 | g881.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 10 | 306 | 0e+00 |
| 3 | g881.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 10 | 306 | 0e+00 |
| 11 | g881.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 27 | 44 | 0e+00 |
| 6 | g881.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 103 | 114 | 2e-07 |
| 10 | g881.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 103 | 114 | 0e+00 |
| 9 | g881.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 148 | 164 | 0e+00 |
| 5 | g881.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 154 | 162 | 2e-07 |
| 4 | g881.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 186 | 205 | 2e-07 |
| 8 | g881.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 186 | 205 | 0e+00 |
| 7 | g881.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 207 | 224 | 0e+00 |
| 1 | g881.t1 | Pfam | PF00106 | short chain dehydrogenase | 26 | 229 | 0e+00 |
| 12 | g881.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 24 | 281 | 0e+00 |
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 transcript has been annotated with K11153 (retinol dehydrogenase 12)
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. There were no conditions that were differentially expressed