General information for g1959.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | isoform | g1959.t1 | 14102561 | 14103519 |
| chr_3 | g1959 | g1959.t1 | exon | g1959.t1.exon1 | 14102561 | 14102568 |
| chr_3 | g1959 | g1959.t1 | cds | g1959.t1.CDS1 | 14102561 | 14102568 |
| chr_3 | g1959 | g1959.t1 | exon | g1959.t1.exon2 | 14102637 | 14103519 |
| chr_3 | g1959 | g1959.t1 | cds | g1959.t1.CDS2 | 14102637 | 14103519 |
| chr_3 | g1959 | g1959.t1 | TTS | g1959.t1 | 14103635 | 14103635 |
| chr_3 | g1959 | g1959.t1 | TSS | g1959.t1 | NA | NA |
Sequences
>g1959.t1 Gene=g1959 Length=891
ATGAATTCAAGCTATACAATAAGATGTGGAAAATATATCAATGACGATGCACAAATTAAA
GACAAAATTGTGATTGTCACTGGATGCAATACTGGTATAGGCAAAGCTACTGCTTTGGAA
CTTGCCAAGCGAGGCGGCAAAATTTATTTCGCATGTCGAAGCGAGAGTAAGGCGATGGAA
GCATTAAATGAGATTAAGCAGTTATCAGGCAATGACAATCTGCATTTTTTACAACTCGAT
TTGGGATCATTAGACTCAATAAGAGAATTTTCGAAAAGGTTTCATGAGTTAGAGAATCGT
TTAGATATTTTGGTAAATAATGCTGGCGTTCTCTCACCACTTGTACAAACAACTGATGGT
TTTGAAGCAAATATTGGAATCAATCACTTAGGGCACTTTTTATTAACAAATTTACTTTTG
GATCTGTTAAAAGCAAGTTCACCAAGCAGAATTATTGTTGTTGCTTCTAAACTTCATAAA
ATTGGATCAATCAATCGAGAAGATTTCAATAGTGAAAAAAGTTTTGCAGGTACTTGGAAA
AGTTATGCAAACAGTAAACTCTGTAATTTACTATTTATGCGAGAATTATCAAAAAGATTA
GAAGGCACAGGTGTAACAATAAATGCTTTATGTCCGGGCGCAGTGAGAACGGAAGCAGGT
CGATCTTTAAATCCTGTGATGAAATTTGTATTAAATCAAGCTATGAAAGTATTTTATAAA
AGTCCTGAATTAGGATGTCAAACAGTTTTATTTCTCAGTGTTGAACCTTCAATAGCAAAA
GAAAGTGGTGGATATTATGTTGACTGCAAGAAAACAGAGCCAAGCAATAATGCAAAGAAC
GATGACGATGCAAAATGGCTTTGGAACATGAGTGAGCAGCTAACTGGATAA
>g1959.t1 Gene=g1959 Length=296
MNSSYTIRCGKYINDDAQIKDKIVIVTGCNTGIGKATALELAKRGGKIYFACRSESKAME
ALNEIKQLSGNDNLHFLQLDLGSLDSIREFSKRFHELENRLDILVNNAGVLSPLVQTTDG
FEANIGINHLGHFLLTNLLLDLLKASSPSRIIVVASKLHKIGSINREDFNSEKSFAGTWK
SYANSKLCNLLFMRELSKRLEGTGVTINALCPGAVRTEAGRSLNPVMKFVLNQAMKVFYK
SPELGCQTVLFLSVEPSIAKESGGYYVDCKKTEPSNNAKNDDDAKWLWNMSEQLTG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1959.t1 | Coils | Coil | Coil | 87 | 107 | - |
| 9 | g1959.t1 | Gene3D | G3DSA:3.40.50.720 | - | 14 | 296 | 1.5E-81 |
| 2 | g1959.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 12 | 296 | 1.2E-110 |
| 3 | g1959.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 12 | 296 | 1.2E-110 |
| 6 | g1959.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 23 | 40 | 5.8E-17 |
| 4 | g1959.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 99 | 110 | 5.8E-17 |
| 7 | g1959.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 182 | 201 | 5.8E-17 |
| 5 | g1959.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 203 | 220 | 5.8E-17 |
| 1 | g1959.t1 | Pfam | PF00106 | short chain dehydrogenase | 22 | 224 | 1.1E-33 |
| 8 | g1959.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 20 | 271 | 7.94E-56 |
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 K00218 (protochlorophyllide reductase)
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.
