General information for g6777.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinol dehydrogenase 11.
Parent gene
- The parent gene g6777 is located on chr_2: 18565069..18566246 (- 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 | g6777 | g6777.t1 | isoform | g6777.t1 | 18565069 | 18566246 |
| chr_2 | g6777 | g6777.t1 | exon | g6777.t1.exon1 | 18565069 | 18565294 |
| chr_2 | g6777 | g6777.t1 | cds | g6777.t1.CDS1 | 18565069 | 18565294 |
| chr_2 | g6777 | g6777.t1 | exon | g6777.t1.exon2 | 18565360 | 18565405 |
| chr_2 | g6777 | g6777.t1 | cds | g6777.t1.CDS2 | 18565360 | 18565405 |
| chr_2 | g6777 | g6777.t1 | exon | g6777.t1.exon3 | 18565467 | 18566089 |
| chr_2 | g6777 | g6777.t1 | cds | g6777.t1.CDS3 | 18565467 | 18566089 |
| chr_2 | g6777 | g6777.t1 | exon | g6777.t1.exon4 | 18566155 | 18566246 |
| chr_2 | g6777 | g6777.t1 | cds | g6777.t1.CDS4 | 18566155 | 18566246 |
| chr_2 | g6777 | g6777.t1 | TSS | g6777.t1 | NA | NA |
| chr_2 | g6777 | g6777.t1 | TTS | g6777.t1 | NA | NA |
Sequences
>g6777.t1 Gene=g6777 Length=987
ATGAGTTCTAACGTTTTAATTACGTTTTCAGTATCAATTTTTGCTGCAATGTTAAGTCTT
AGTCTTTTTATCATAATCATTATAATGATAAGAAATTATATGCAAGGTGGAAAATATAAG
AAATCTACTTTGATCGATGGAAAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGA
AAAGAGACTGCCATTGACTTGGCTAAACGTGGTGGAAAAATTTATATCGCATGTCGCAAT
GAAAAACGCGGTCAAAATGCTCAAATGGAAATTATTGAAAAAAGTAGTAATATGAATGTT
CACTTTCTGCAACTTGATTTAGCATCGATGGATTCTATTCGTAAATTTTCACGGAAGTTT
CATGAATTAGAGTCTCAATTGCATATTCTCATAAACAATGCAGGTGTAATGGCTTGTCCA
AAATCATATACAAAAGATGGATTTGAAATGCACATGGGAGTTAATCATTTAGGACATTTT
TTACTTACAAATCTTTTACTTGACATTTTAAAAAACACACCAAATAGTCGTATCGTAAAT
GTTTCTAGTTTATTTCATATCGTTGGATTTATATGGAAGAGTAACTTTTTTGGCGAAAAA
TTTTATTTTCGTTGGCATGCTTATGCTACGAGTAAGTTAGCAAATATTCTTTTCACAAGA
GAATTAGCAAAACGTTTGAAATCGTCAAATACCACTGCAAACTCACTTCATCCAGGTGCT
GTGCATAGTAATTTACAACGTCATGTAAGCAGTGTTATTAAAATTTTAACTACACCGTTT
CAATGGATACTTTTCAAAGACACTCTAGCAGGAGCTCAAACGACAATTTTTTTATCTGTT
GACCCATCATTGGATAAAGTTACTGGAAAATATTTTAGTGATTGTCGACAGTGTTCTCCA
CTTTTTACCGCCAAAAATGACGTCCTTGCAAAATGGCTATGGGAAAAAAGCGAAGAACTA
ACAGGCCTCGCAGTAAAAGAAATATAA
>g6777.t1 Gene=g6777 Length=328
MSSNVLITFSVSIFAAMLSLSLFIIIIIMIRNYMQGGKYKKSTLIDGKIVIITGANTGIG
KETAIDLAKRGGKIYIACRNEKRGQNAQMEIIEKSSNMNVHFLQLDLASMDSIRKFSRKF
HELESQLHILINNAGVMACPKSYTKDGFEMHMGVNHLGHFLLTNLLLDILKNTPNSRIVN
VSSLFHIVGFIWKSNFFGEKFYFRWHAYATSKLANILFTRELAKRLKSSNTTANSLHPGA
VHSNLQRHVSSVIKILTTPFQWILFKDTLAGAQTTIFLSVDPSLDKVTGKYFSDCRQCSP
LFTAKNDVLAKWLWEKSEELTGLAVKEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g6777.t1 | Gene3D | G3DSA:3.40.50.720 | - | 38 | 325 | 5.4E-80 |
| 2 | g6777.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 19 | 323 | 2.0E-126 |
| 3 | g6777.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 19 | 323 | 2.0E-126 |
| 10 | g6777.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 49 | 66 | 5.5E-17 |
| 6 | g6777.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 125 | 136 | 4.6E-8 |
| 11 | g6777.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 125 | 136 | 5.5E-17 |
| 8 | g6777.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 170 | 186 | 5.5E-17 |
| 5 | g6777.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 176 | 184 | 4.6E-8 |
| 4 | g6777.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 208 | 227 | 4.6E-8 |
| 7 | g6777.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 208 | 227 | 5.5E-17 |
| 9 | g6777.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 229 | 246 | 5.5E-17 |
| 1 | g6777.t1 | Pfam | PF00106 | short chain dehydrogenase | 48 | 249 | 5.6E-35 |
| 16 | g6777.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 17 | g6777.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 30 | - |
| 15 | g6777.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 31 | 328 | - |
| 13 | g6777.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 46 | 300 | 1.0E-57 |
| 12 | g6777.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
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 K11152 (retinol dehydrogenase 11)
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. There were no conditions that were differentially expressed