General information for g6779.t2
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinol dehydrogenase 14.
Parent gene
- The parent gene g6779 is located on chr_2: 18572612..18575178 (+ 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_2 | g6779 | g6779.t2 | TSS | g6779.t2 | 18571442 | 18571442 |
| chr_2 | g6779 | g6779.t2 | isoform | g6779.t2 | 18571497 | 18572612 |
| chr_2 | g6779 | g6779.t2 | exon | g6779.t2.exon1 | 18571497 | 18572256 |
| chr_2 | g6779 | g6779.t2 | cds | g6779.t2.CDS1 | 18571848 | 18572256 |
| chr_2 | g6779 | g6779.t2 | exon | g6779.t2.exon2 | 18572320 | 18572612 |
| chr_2 | g6779 | g6779.t2 | cds | g6779.t2.CDS2 | 18572320 | 18572612 |
| chr_2 | g6779 | g6779.t2 | TTS | g6779.t2 | NA | NA |
Sequences
>g6779.t2 Gene=g6779 Length=1053
ATGAAAACCTTTTTAAAAAGCTTGTAAGTGACGTTATTAAATTTTTTATTTTCATTTATT
ATTAAATGATTTTCAGCTTAAATATCGTCAATAAACCTATTTATAAGAAAAATACAAAAA
TCGATAATAAAGTCGTTATAATAACAGGTTTGTTAAATTTATTAGAATTTTTGTTCTTAA
CAAGAAACAAAAATTAAATTTTTAGGAGGAAATTCAGGAATCGGAAAAGAAACAGCAGTT
GATTTAGCAAAACGTGGTGGAAAAATCTACATTGCTTGTAGAGATGTTATTCGTAGTCAA
CAAGATCTTGAAGAGATCAAAGGAAGAGCCAAAGCTTCGAAAGTCTATCTTATGGAACTT
GACCTTGCTTCAATAAAATCAATCAGAAAATTTTCAAGAGAATTTCATGAACGAGAAAAA
AAATTACATATTCTCATAAATAATGCAGGTGTAATGGCTTGCCCAAAATCATATACAAAA
GATGGATTTGAAATGCAAATGGGAGTTAATCATTTAGGTCATTTCTTGCTAACAAATCTG
CTTCTTGATATGCTTAAATTATCTGCACCAAGTCGAATCGTCGTTGTATCTTCTTCAGGC
CACAAGCTTTCTGGAATAAATCGAGATGATTTTATGAGTGAAAAGAGTTATAATAAAATA
AAAGCTTATGGTCAAAGTAAATTAGCAAACATTTTATTTGCTCTGGAATTATCGAGAAGA
CTTCATGGTTTAGATGTAACTTGTAACTCGCTACATCCTGGACTTGTACATACAAATCTT
GGAAGACATATGAACTCGCGCTTTCGTCCAATTTATGGAAAAGTTTTGAAACCATTTTAC
AAAACTACATTTGAAGGAGCTCAAACACAAATTCGGTTAGCAGTTGATCCTGATTTAGAA
GGTGTAACAGGAAAATATTTTGTTGATTGTGAAGAAGCAACACCATCAGAAGAAGCTCAA
AGTTATGAAACAGCAGCATGGTTATGGAACAAAAGTACTCAATTAATTTATGATAAATTT
AAGAAATTTGATTTAGACAATAAAAATAATTAA
>g6779.t2 Gene=g6779 Length=233
MELDLASIKSIRKFSREFHEREKKLHILINNAGVMACPKSYTKDGFEMQMGVNHLGHFLL
TNLLLDMLKLSAPSRIVVVSSSGHKLSGINRDDFMSEKSYNKIKAYGQSKLANILFALEL
SRRLHGLDVTCNSLHPGLVHTNLGRHMNSRFRPIYGKVLKPFYKTTFEGAQTQIRLAVDP
DLEGVTGKYFVDCEEATPSEEAQSYETAAWLWNKSTQLIYDKFKKFDLDNKNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6779.t2 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 225 | 0 |
| 2 | g6779.t2 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 2 | 219 | 0 |
| 3 | g6779.t2 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 2 | 219 | 0 |
| 1 | g6779.t2 | Pfam | PF00106 | short chain dehydrogenase | 2 | 148 | 0 |
| 4 | g6779.t2 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 197 | 0 |
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. There were no conditions that were differentially expressed