General information for g1959.t3
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Retinol dehydrogenase 14.
Parent gene
- The parent gene g1959 is located on chr_3: 14103120..14112263 (+ 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 | g1959 | g1959.t3 | TSS | g1959.t3 | 14102638 | 14102638 |
| chr_3 | g1959 | g1959.t3 | isoform | g1959.t3 | 14102640 | 14103519 |
| chr_3 | g1959 | g1959.t3 | exon | g1959.t3.exon1 | 14102640 | 14103519 |
| chr_3 | g1959 | g1959.t3 | cds | g1959.t3.CDS1 | 14102803 | 14103519 |
| chr_3 | g1959 | g1959.t3 | TTS | g1959.t3 | 14103635 | 14103635 |
Sequences
>g1959.t3 Gene=g1959 Length=880
CTATACAATAAGATGTGGAAAATATATCAATGACGATGCACAAATTAAAGACAAAATTGT
GATTGTCACTGGATGCAATACTGGTATAGGCAAAGCTACTGCTTTGGAACTTGCCAAGCG
AGGCGGCAAAATTTATTTCGCATGTCGAAGCGAGAGTAAGGCGATGGAAGCATTAAATGA
GATTAAGCAGTTATCAGGCAATGACAATCTGCATTTTTTACAACTCGATTTGGGATCATT
AGACTCAATAAGAGAATTTTCGAAAAGGTTTCATGAGTTAGAGAATCGTTTAGATATTTT
GGTAAATAATGCTGGCGTTCTCTCACCACTTGTACAAACAACTGATGGTTTTGAAGCAAA
TATTGGAATCAATCACTTAGGGCACTTTTTATTAACAAATTTACTTTTGGATCTGTTAAA
AGCAAGTTCACCAAGCAGAATTATTGTTGTTGCTTCTAAACTTCATAAAATTGGATCAAT
CAATCGAGAAGATTTCAATAGTGAAAAAAGTTTTGCAGGTACTTGGAAAAGTTATGCAAA
CAGTAAACTCTGTAATTTACTATTTATGCGAGAATTATCAAAAAGATTAGAAGGCACAGG
TGTAACAATAAATGCTTTATGTCCGGGCGCAGTGAGAACGGAAGCAGGTCGATCTTTAAA
TCCTGTGATGAAATTTGTATTAAATCAAGCTATGAAAGTATTTTATAAAAGTCCTGAATT
AGGATGTCAAACAGTTTTATTTCTCAGTGTTGAACCTTCAATAGCAAAAGAAAGTGGTGG
ATATTATGTTGACTGCAAGAAAACAGAGCCAAGCAATAATGCAAAGAACGATGACGATGC
AAAATGGCTTTGGAACATGAGTGAGCAGCTAACTGGATAA
>g1959.t3 Gene=g1959 Length=238
MEALNEIKQLSGNDNLHFLQLDLGSLDSIREFSKRFHELENRLDILVNNAGVLSPLVQTT
DGFEANIGINHLGHFLLTNLLLDLLKASSPSRIIVVASKLHKIGSINREDFNSEKSFAGT
WKSYANSKLCNLLFMRELSKRLEGTGVTINALCPGAVRTEAGRSLNPVMKFVLNQAMKVF
YKSPELGCQTVLFLSVEPSIAKESGGYYVDCKKTEPSNNAKNDDDAKWLWNMSEQLTG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1959.t3 | Coils | Coil | Coil | 29 | 49 | - |
| 8 | g1959.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 238 | 4.3E-62 |
| 2 | g1959.t3 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 3 | 238 | 1.4E-87 |
| 3 | g1959.t3 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 3 | 238 | 1.4E-87 |
| 6 | g1959.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 41 | 52 | 2.7E-9 |
| 4 | g1959.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 124 | 143 | 2.7E-9 |
| 5 | g1959.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 145 | 162 | 2.7E-9 |
| 1 | g1959.t3 | Pfam | PF00106 | short chain dehydrogenase | 3 | 166 | 1.9E-20 |
| 7 | g1959.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 3 | 213 | 2.91E-39 |
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.
