General information for g16654.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Epidermal retinol dehydrogenase 2.
Parent gene
- The parent gene g16654 is located on chr_4: 10414677..10415956 (- 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_4 | g16654 | g16654.t1 | TTS | g16654.t1 | 10414152 | 10414152 |
| chr_4 | g16654 | g16654.t1 | isoform | g16654.t1 | 10414221 | 10415956 |
| chr_4 | g16654 | g16654.t1 | exon | g16654.t1.exon1 | 10414221 | 10414664 |
| chr_4 | g16654 | g16654.t1 | cds | g16654.t1.CDS1 | 10414221 | 10414664 |
| chr_4 | g16654 | g16654.t1 | exon | g16654.t1.exon2 | 10415251 | 10415558 |
| chr_4 | g16654 | g16654.t1 | cds | g16654.t1.CDS2 | 10415251 | 10415558 |
| chr_4 | g16654 | g16654.t1 | exon | g16654.t1.exon3 | 10415633 | 10415882 |
| chr_4 | g16654 | g16654.t1 | cds | g16654.t1.CDS3 | 10415633 | 10415882 |
| chr_4 | g16654 | g16654.t1 | exon | g16654.t1.exon4 | 10415939 | 10415956 |
| chr_4 | g16654 | g16654.t1 | cds | g16654.t1.CDS4 | 10415939 | 10415956 |
| chr_4 | g16654 | g16654.t1 | TSS | g16654.t1 | 10415963 | 10415963 |
Sequences
>g16654.t1 Gene=g16654 Length=1020
ATGAGTGCTAGAGGAGCTGACTTTAGAGCACAAAGATCTTCCCAACGATCACATGAAATC
CATGGATGGTTAAAGCACATAGGAAAACTAGGATTTCCATTGCAAATTCTTCTCAAATCA
TATCAATGTTTTGTTGTTTGGTGTGATGTTATGACACTCATTATCAGATCTTATTTTGCA
ATTCTTCAGACAATTTTGTGTTTTTTTATTCCTGTATCAAGAAAAAGTTTGAAGACTGAA
GTTGCAGTTGTTGTTGGATCATCAAGAGGAGTTGGCAGAGAAATCGCTTACAAATTAAGT
TCATTGAGAGCAACAGTAGTATGCATAGACATTCAAGATCCAGATGATGAAACAGTTTCA
AAAACAATCAGAGCTGAAGGTGCAAATGCTTATTATTTTCAATGTGATATTTCAATTAGA
GACCAAGTTGACATAACAGTCAGCAGAATTGAAAAAGAAATTGGTGGAATTTCCATGCTT
TATCATTGTTGCTCTCTACCTTCACCAAGATGTGTTTCTACTAATCCTCCTTCAGTTAAA
GCAACTTTGGATGTTTCTGTTACGAGCTATTTTTATTTACTCGATGCTATTCTTCCACAT
ATGAAGACAAATAACAAAGGTCATATTGTATTTCTTACGTCTGTTGCTGCGATTAGTGGA
TTTACACAGCAACTTGCATTAAGTGTATCACAATTCGCCATACAAGGTCTTTATGAGTCA
ATTGTTGAAGAATTAAGAATATCGAGATGTGATCAAATTATAAAAACAACTTTGGTTCAT
ATTTATCCATTTATTGTCAGTGAAAATTTCTCTAATGATATTCGATTTAGAGTTCCAGGA
TTTTTTGGTTCAATTCGAGCTGATATTGCTGCTGAAAAAATTATTGATGGTGTAAGAATG
AATGCAAGTGAAATAAGCATTCCAAGTTATTGTTTGTACATCAGTCATGTACTGAAAATT
TTACCAAGAAAAGTAACTTTAATGTTAAGAGAATTTCTTGATACTGGAGTTGATTTTTGA
>g16654.t1 Gene=g16654 Length=339
MSARGADFRAQRSSQRSHEIHGWLKHIGKLGFPLQILLKSYQCFVVWCDVMTLIIRSYFA
ILQTILCFFIPVSRKSLKTEVAVVVGSSRGVGREIAYKLSSLRATVVCIDIQDPDDETVS
KTIRAEGANAYYFQCDISIRDQVDITVSRIEKEIGGISMLYHCCSLPSPRCVSTNPPSVK
ATLDVSVTSYFYLLDAILPHMKTNNKGHIVFLTSVAAISGFTQQLALSVSQFAIQGLYES
IVEELRISRCDQIIKTTLVHIYPFIVSENFSNDIRFRVPGFFGSIRADIAAEKIIDGVRM
NASEISIPSYCLYISHVLKILPRKVTLMLREFLDTGVDF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g16654.t1 | Gene3D | G3DSA:3.40.50.720 | - | 70 | 335 | 4.6E-40 |
| 2 | g16654.t1 | PANTHER | PTHR24322 | PKSB | 35 | 338 | 1.9E-61 |
| 3 | g16654.t1 | PANTHER | PTHR24322:SF730 | FI02989P-RELATED | 35 | 338 | 1.9E-61 |
| 4 | g16654.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 81 | 98 | 9.0E-9 |
| 5 | g16654.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 201 | 217 | 9.0E-9 |
| 6 | g16654.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 227 | 246 | 9.0E-9 |
| 1 | g16654.t1 | Pfam | PF00106 | short chain dehydrogenase | 81 | 248 | 1.4E-30 |
| 10 | g16654.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 43 | - |
| 11 | g16654.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 70 | - |
| 9 | g16654.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 71 | 339 | - |
| 7 | g16654.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 73 | 331 | 4.51E-35 |
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.
