General information for g1959.t4
Yuki Yoshida
22/1/2022
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.t4 | TSS | g1959.t4 | 14102638 | 14102638 |
| chr_3 | g1959 | g1959.t4 | isoform | g1959.t4 | 14103120 | 14112263 |
| chr_3 | g1959 | g1959.t4 | exon | g1959.t4.exon1 | 14103120 | 14103587 |
| chr_3 | g1959 | g1959.t4 | cds | g1959.t4.CDS1 | 14103205 | 14103519 |
| chr_3 | g1959 | g1959.t4 | exon | g1959.t4.exon2 | 14112246 | 14112263 |
| chr_3 | g1959 | g1959.t4 | TTS | g1959.t4 | NA | NA |
Sequences
>g1959.t4 Gene=g1959 Length=486
CAATCGAGAAGATTTCAATAGTGAAAAAAGTTTTGCAGGTACTTGGAAAAGTTATGCAAA
CAGTAAACTCTGTAATTTACTATTTATGCGAGAATTATCAAAAAGATTAGAAGGCACAGG
TGTAACAATAAATGCTTTATGTCCGGGCGCAGTGAGAACGGAAGCAGGTCGATCTTTAAA
TCCTGTGATGAAATTTGTATTAAATCAAGCTATGAAAGTATTTTATAAAAGTCCTGAATT
AGGATGTCAAACAGTTTTATTTCTCAGTGTTGAACCTTCAATAGCAAAAGAAAGTGGTGG
ATATTATGTTGACTGCAAGAAAACAGAGCCAAGCAATAATGCAAAGAACGATGACGATGC
AAAATGGCTTTGGAACATGAGTGAGCAGCTAACTGGATAAAAATAAACAGCACGAGAGAG
AATAAAATGTATGATTTACACAATGTTATTTATTTAATTGGCCTTGAGTTTTATCATTAA
GAGGCA
>g1959.t4 Gene=g1959 Length=104
MRELSKRLEGTGVTINALCPGAVRTEAGRSLNPVMKFVLNQAMKVFYKSPELGCQTVLFL
SVEPSIAKESGGYYVDCKKTEPSNNAKNDDDAKWLWNMSEQLTG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g1959.t4 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 104 | 0 |
| 1 | g1959.t4 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 2 | 104 | 0 |
| 2 | g1959.t4 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 2 | 104 | 0 |
| 3 | g1959.t4 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 102 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
