General information for g1960.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Retinol dehydrogenase 12.
Parent gene
- The parent gene g1960 is located on chr_3: 14105943..14106332 (+ 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 | g1960 | g1960.t1 | isoform | g1960.t1 | 14105943 | 14106332 |
| chr_3 | g1960 | g1960.t1 | exon | g1960.t1.exon1 | 14105943 | 14106332 |
| chr_3 | g1960 | g1960.t1 | cds | g1960.t1.CDS1 | 14105943 | 14106332 |
| chr_3 | g1960 | g1960.t1 | TSS | g1960.t1 | NA | NA |
| chr_3 | g1960 | g1960.t1 | TTS | g1960.t1 | NA | NA |
Sequences
>g1960.t1 Gene=g1960 Length=390
ATGTATGTCAATGACAATGCTCAAATCAAAGATAAGATTGTCATTATAACCGGTTCTAAT
ACTGGAATTGGAAAAGCTACTGCACTTCAATTAGCAAAAAGAGGTGGAAAAATTTATTTT
GCATGTCGAAGTAAAGAGAGAGGAATTAAAGCATTGAATGAAATTAAAGAGCAGTCGGGC
AATGAAAATCTTCACTTTTTAAAGCTGGACTTAAATTCATTAGAGTCTGTGAGAGAATTT
GCAAAAAAATTTCACGAACTGGAAAATCGTTTAGATATTTTGATAAATAACGCAGCCGTT
TTAATGCCTCCTACAGAACAAACTGTCGATGGATTCGAAAAAATTAAAAAAATATATCAA
TCTCGACACCTTAAGTCGTTTTTTTTTTAA
>g1960.t1 Gene=g1960 Length=129
MYVNDNAQIKDKIVIITGSNTGIGKATALQLAKRGGKIYFACRSKERGIKALNEIKEQSG
NENLHFLKLDLNSLESVREFAKKFHELENRLDILINNAAVLMPPTEQTVDGFEKIKKIYQ
SRHLKSFFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1960.t1 | Coils | Coil | Coil | 77 | 97 | - |
| 7 | g1960.t1 | Gene3D | G3DSA:3.40.50.720 | - | 2 | 127 | 2.3E-33 |
| 2 | g1960.t1 | PANTHER | PTHR43157 | PHOSPHATIDYLINOSITOL-GLYCAN BIOSYNTHESIS CLASS F PROTEIN-RELATED | 6 | 117 | 1.6E-37 |
| 3 | g1960.t1 | PANTHER | PTHR43157:SF45 | WW DOMAIN-CONTAINING OXIDOREDUCTASE-LIKE PROTEIN | 6 | 117 | 1.6E-37 |
| 4 | g1960.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 13 | 30 | 1.6E-8 |
| 5 | g1960.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 89 | 100 | 1.6E-8 |
| 1 | g1960.t1 | Pfam | PF00106 | short chain dehydrogenase | 12 | 105 | 3.1E-19 |
| 6 | g1960.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 6 | 115 | 1.74E-28 |
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.
