General information for g1961.t1
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 g1961 is located on chr_3: 14106650..14107045 (+ 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 | g1961 | g1961.t1 | isoform | g1961.t1 | 14106650 | 14107045 |
| chr_3 | g1961 | g1961.t1 | exon | g1961.t1.exon1 | 14106650 | 14107045 |
| chr_3 | g1961 | g1961.t1 | cds | g1961.t1.CDS1 | 14106650 | 14107045 |
| chr_3 | g1961 | g1961.t1 | TSS | g1961.t1 | NA | NA |
| chr_3 | g1961 | g1961.t1 | TTS | g1961.t1 | NA | NA |
Sequences
>g1961.t1 Gene=g1961 Length=396
ATGGGTGTCAATCATTTGGGTCATTTTTTGCTAACTCACTTGTTGCTTGATTTATTAAAA
GCAAGTTCTCCAAGTCGAATTGTTGTTGTAGCTTCAGATGCACACAAATACGGAAATATC
AACAAAGAAGATTTCAATAGTGAAAAACAAACTGGAAAAGGTTTTTCTGATTCATTGAAA
GCATACGGAACAAGCAAAATTGCAAACATACTTTTTACTCGTGAATTATCGAAAAGATTA
AATAGGACAGGAATTGTAGTCAATACACTCTGTCCCGGAAATGTGCATACTGAAGCAACA
CGATATTTGGGTACTGTTGTTCATTTTCTTTTGAGCACATTGAAAAAATATTTCAAAAAA
ACACCTGAGGAGGGATGTCAAACGATTTTAATGTAG
>g1961.t1 Gene=g1961 Length=131
MGVNHLGHFLLTHLLLDLLKASSPSRIVVVASDAHKYGNINKEDFNSEKQTGKGFSDSLK
AYGTSKIANILFTRELSKRLNRTGIVVNTLCPGNVHTEATRYLGTVVHFLLSTLKKYFKK
TPEEGCQTILM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1961.t1 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 131 | 1.3E-33 |
| 2 | g1961.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 1 | 130 | 8.2E-43 |
| 3 | g1961.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 1 | 130 | 8.2E-43 |
| 5 | g1961.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 19 | 35 | 4.2E-6 |
| 6 | g1961.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 62 | 81 | 4.2E-6 |
| 4 | g1961.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 83 | 100 | 4.2E-6 |
| 1 | g1961.t1 | Pfam | PF00106 | short chain dehydrogenase | 57 | 102 | 1.6E-8 |
| 11 | g1961.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 12 | g1961.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 13 | g1961.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 16 | - |
| 14 | g1961.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 10 | g1961.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 131 | - |
| 7 | g1961.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 1 | 130 | 2.67E-23 |
| 8 | g1961.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
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.
