General information for g5168.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Epidermal retinol dehydrogenase 2.
Parent gene
- The parent gene g5168 is located on chr_2: 7418327..7424243 (+ 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_2 | g5168 | g5168.t1 | TSS | g5168.t1 | 7418063 | 7418063 |
| chr_2 | g5168 | g5168.t1 | isoform | g5168.t1 | 7418327 | 7424243 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon1 | 7418327 | 7418473 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS1 | 7418327 | 7418473 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon2 | 7421923 | 7421962 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS2 | 7421923 | 7421962 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon3 | 7422025 | 7422102 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS3 | 7422025 | 7422102 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon4 | 7423169 | 7423305 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS4 | 7423169 | 7423305 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon5 | 7423367 | 7423392 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS5 | 7423367 | 7423392 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon6 | 7423454 | 7423526 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS6 | 7423454 | 7423526 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon7 | 7423599 | 7423641 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS7 | 7423599 | 7423641 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon8 | 7423705 | 7423901 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS8 | 7423705 | 7423901 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon9 | 7423959 | 7424080 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS9 | 7423959 | 7424080 |
| chr_2 | g5168 | g5168.t1 | exon | g5168.t1.exon10 | 7424141 | 7424243 |
| chr_2 | g5168 | g5168.t1 | cds | g5168.t1.CDS10 | 7424141 | 7424243 |
| chr_2 | g5168 | g5168.t1 | TTS | g5168.t1 | 7424337 | 7424337 |
Sequences
>g5168.t1 Gene=g5168 Length=966
ATGAGGCAGGGCCTAATCTATGAAAACGCATTTGAATATGTTTACACACTTTTATTTGAT
ATATTTGTTTGTTCTCTAAAATCAACCTTTTATTTGCTTGAGACAATTTTTCTAACTCTT
TTGCCAGATAAGCTGCGACGTAAGAAGGATGTCTCTGGACAAATTGTGTTGATAACAGGA
GGAGGAGGCGGAGTTGGTCGACACATTGCACTTAATTTTGCACGCCTCAACGCAAAGATA
ATAATCTGGGATGTAAATCGTGAAGCAATCAACGCAACATGTGATGCTCTAAAAACTGAA
GGTTTCGAATGTGCTTCATATATTGTCGACATCTCTGATCGGGAAAAGGTATATGAAGCG
GCTAAAAGGGTTAAAGAGGAAATTGGAAAGGTCGATATTTTGGTCAACAATGCAGGGATT
GTTACATGTCGTCCACTTTTTGAAATTCCCGACAAAGCAATAGAAGCAACATATGGAGTC
AATATCTTGAGTCATTATTGGACCGTTAAAGCATTTTTACCGGATATGATTGCTAACAAA
CGAGGCCATATTGTAACTGTAAGCAGTGTAACAGGATTGATGGGGACTTATGCATGTACT
GATTATTCAGCTACTAAATTCGCAACTGTTGGCTTCCATGAGAGTTTATACAGCGAGTTG
AAATATCATGGTCATGATTACATTGGAATGACTTTAGTATGCCCTTACTATATCAACACT
CAATTATTTAGCGGTGTTAAGCCTCGACTGTTTCCTATGTTGGAGCCAAAATATGTTGCT
GATAAACTTGTAGAATCAACATTAAAGAATGAAGTCAATTGTACTCTTCCTAATTCTGTG
AGGATGTTGCTTCCACTTAAATGTCTTTTACCAGCAAAGACATGTTGGGAATTGATGGTA
AGAATTATGAAAGGACCACAATCGATGAGTCTTTATAAAGGAAGAGGAAAAGCAAAATCA
GGATAA
>g5168.t1 Gene=g5168 Length=321
MRQGLIYENAFEYVYTLLFDIFVCSLKSTFYLLETIFLTLLPDKLRRKKDVSGQIVLITG
GGGGVGRHIALNFARLNAKIIIWDVNREAINATCDALKTEGFECASYIVDISDREKVYEA
AKRVKEEIGKVDILVNNAGIVTCRPLFEIPDKAIEATYGVNILSHYWTVKAFLPDMIANK
RGHIVTVSSVTGLMGTYACTDYSATKFATVGFHESLYSELKYHGHDYIGMTLVCPYYINT
QLFSGVKPRLFPMLEPKYVADKLVESTLKNEVNCTLPNSVRMLLPLKCLLPAKTCWELMV
RIMKGPQSMSLYKGRGKAKSG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5168.t1 | CDD | cd05339 | 17beta-HSDXI-like_SDR_c | 55 | 293 | 7.47952E-100 |
| 13 | g5168.t1 | Gene3D | G3DSA:3.40.50.720 | - | 42 | 304 | 1.3E-63 |
| 2 | g5168.t1 | PANTHER | PTHR24322 | PKSB | 11 | 320 | 9.2E-152 |
| 3 | g5168.t1 | PANTHER | PTHR24322:SF729 | MIP05442P | 11 | 320 | 9.2E-152 |
| 10 | g5168.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 55 | 72 | 2.9E-23 |
| 5 | g5168.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 129 | 140 | 4.2E-11 |
| 11 | g5168.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 129 | 140 | 2.9E-23 |
| 8 | g5168.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 176 | 192 | 2.9E-23 |
| 6 | g5168.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 182 | 190 | 4.2E-11 |
| 4 | g5168.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 202 | 221 | 4.2E-11 |
| 7 | g5168.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 202 | 221 | 2.9E-23 |
| 9 | g5168.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 226 | 243 | 2.9E-23 |
| 1 | g5168.t1 | Pfam | PF00106 | short chain dehydrogenase | 54 | 244 | 1.1E-48 |
| 15 | g5168.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 12 | - |
| 16 | g5168.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 41 | - |
| 14 | g5168.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 42 | 321 | - |
| 12 | g5168.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 49 | 306 | 3.26E-61 |
| 18 | g5168.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5168/g5168.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5168.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
## [1] "No matching GO terms"KEGG
Orthology
- This transcript has been annotated with K15734 (all-trans-retinol dehydrogenase (NAD+))
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