General information for g6778.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinol dehydrogenase 12.
Parent gene
- The parent gene g6778 is located on chr_2: 18569895..18571045 (- 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 | g6778 | g6778.t1 | isoform | g6778.t1 | 18567774 | 18571045 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon1 | 18567774 | 18568005 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS1 | 18567774 | 18568005 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon2 | 18568066 | 18568111 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS2 | 18568066 | 18568111 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon3 | 18568168 | 18568719 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS3 | 18568168 | 18568719 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon4 | 18568784 | 18568854 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS4 | 18568784 | 18568854 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon5 | 18569494 | 18569543 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS5 | 18569494 | 18569543 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon6 | 18569895 | 18570102 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS6 | 18569895 | 18570102 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon7 | 18570163 | 18570208 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS7 | 18570163 | 18570208 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon8 | 18570264 | 18570886 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS8 | 18570264 | 18570886 |
| chr_2 | g6778 | g6778.t1 | exon | g6778.t1.exon9 | 18570951 | 18571045 |
| chr_2 | g6778 | g6778.t1 | cds | g6778.t1.CDS9 | 18570951 | 18571045 |
| chr_2 | g6778 | g6778.t1 | TSS | g6778.t1 | 18571007 | 18571007 |
| chr_2 | g6778 | g6778.t1 | TTS | g6778.t1 | NA | NA |
Sequences
>g6778.t1 Gene=g6778 Length=1923
ATGGAGTTTTTTAAAAATCTCAACTCCACATTAACTTTAGTCATCATTGTAACTTCTGCT
TTAATATTTGTTTGCGTTGTTTTATTGCTGTTCAGAATGTGGATGCAAGGAGGTCAATTT
AGAAAAGACACTAGAATCGATGGAAAAATTGTAATCATCACCGGTGCAAATGCAGGCATC
GGAAAAGAGACTGCCATTGACTTGGCAAAACGTGGTGGAAAAATTTATATTGCATGTCGC
GATGAAAAACGCGGTGAAAATGCTCAAATGGAAATTATTGAAAAAAGTGGCAGTGACAAA
GTTCATTTCATGCAACTTGATTTAGCTTCATTACAATCTGTTCGAGAATTTGTACAAAAA
TTTCATCAAGTTGAGAGTAAATTGCATATTCTGATAAATAATGCAGGTGTAATGGCTTGT
CCAAAATCATATACAGCTGATGGATATGAATTGCAATTTGGAACTAATCATTTGGGGCAT
TTTTTACTCACAAATTTATTACTTGATTTGTTAAAAGCCGGCGCACCAAGTCGAATTATT
AATGTCTCAAGTATTTTACATAACATAGGCAGAATAAACAAGCAAGATTTGATGCATCAA
GAAAGTTATTGGAAGTGGCTTGTTTATGGACAAAGTAAACTTGCAAACATTTTGTTTACA
CGTGAATTGGCAAAACAACTCGATGGCACTGGTGTTACAGTGAACTCACTTCATCCAGGA
GCTGTTAACACGGAATTATCACGAAACTTAGATTTATGCTCTAAATTCATTTTTCATCCT
GTAAAATGGTTGGTCTTCAAAACACCCAAATCTGGAGCTCAAACTCAAATTTATTTGGCC
GTTGACCCCGAACTTGAAAATGTAACAGGAAAGTATTTTGCTGATTGCAAAGAAAAAAGT
CCTTCAAGTGCGGCACGTGATGACGAAACCGCGCGTTGGTTATGGAAAGAAAGTGAAAAA
CTTACCAACATGCGTAATGAGAAAGCACCAAACATTTCTCAACTTCTTCACAGTCGTCGT
TTAAAATGGATACGAGGAGAAGAATTCACAAGTAATGTAAGAATTGATGGTAAAGTTGTT
ATCATTACTGGTGCAAATACGGGGATCGGGAAAGAAACCGCCATTGATTTAGCTAAACGC
GGTGGAAAAATTTATATTGCATGTCGTGATCCCGTGCGTGGTGTAGAAGCATTGAAAGAA
ATTCAAGATTTAAGTGAGAGCAGTAATGTGTATTTTTTACAACTTGACCTCGCTCAACTT
GAATCAATTCGTCAATTTTCAAAAAGATTTCATGAAAAAGAAAATCAATTACACATACTA
ATCAATAATGCTGGTGTAATGGCATGTAAACGAGCACAAACAAGAGATGGATTTGAGATG
CAAATAGGAGTGAATCATATGGGTCATTTTTTGCTTACACACTTACTACTTAATACATTA
AAAGAATCAGCTCCTGCACGCATAATAAACGTCTCAAGCCTTTATCATATTTTTGGCTAT
ATAAATAAAAATGACTTAAACAGTGAAAAACATTACTGGCGTTGGCTTGCTTATGCTCAA
AGTAAACTTGCAAATATTCTATTTACACGTGAATTGGCAAAACGACTTGATGGGACAAAC
ATTACAGTGAATGCGCTACATCCCGGATGTGTTAATACTGAATTGACAAGAAATTTGGAT
TGGTTTACAAGAACTTTCGTTCGACCATGCCAAGAATTCATTTTTAAATCTCCATCAGCG
GGTGCTCAAACACAAATTCGCCTTGCAATTGATCCTGAACTTGAAAATGTCACTGGAAAA
TATTTTGCAGATTGTAAAGAAAAAACACCTTCACGAAGAGCTCTCAATGATGAAACAGCA
GAATGGCTTTGGAATATTAGCGAAGAGTGGACAGGAATGTCAATTCCCAACACAGTCGCT
TGA
>g6778.t1 Gene=g6778 Length=640
MEFFKNLNSTLTLVIIVTSALIFVCVVLLLFRMWMQGGQFRKDTRIDGKIVIITGANAGI
GKETAIDLAKRGGKIYIACRDEKRGENAQMEIIEKSGSDKVHFMQLDLASLQSVREFVQK
FHQVESKLHILINNAGVMACPKSYTADGYELQFGTNHLGHFLLTNLLLDLLKAGAPSRII
NVSSILHNIGRINKQDLMHQESYWKWLVYGQSKLANILFTRELAKQLDGTGVTVNSLHPG
AVNTELSRNLDLCSKFIFHPVKWLVFKTPKSGAQTQIYLAVDPELENVTGKYFADCKEKS
PSSAARDDETARWLWKESEKLTNMRNEKAPNISQLLHSRRLKWIRGEEFTSNVRIDGKVV
IITGANTGIGKETAIDLAKRGGKIYIACRDPVRGVEALKEIQDLSESSNVYFLQLDLAQL
ESIRQFSKRFHEKENQLHILINNAGVMACKRAQTRDGFEMQIGVNHMGHFLLTHLLLNTL
KESAPARIINVSSLYHIFGYINKNDLNSEKHYWRWLAYAQSKLANILFTRELAKRLDGTN
ITVNALHPGCVNTELTRNLDWFTRTFVRPCQEFIFKSPSAGAQTQIRLAIDPELENVTGK
YFADCKEKTPSRRALNDETAEWLWNISEEWTGMSIPNTVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g6778.t1 | Gene3D | G3DSA:3.40.50.720 | - | 40 | 327 | 4.0E-90 |
| 18 | g6778.t1 | Gene3D | G3DSA:3.40.50.720 | - | 349 | 635 | 7.0E-88 |
| 4 | g6778.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 16 | 324 | 9.2E-279 |
| 6 | g6778.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 16 | 324 | 9.2E-279 |
| 3 | g6778.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 341 | 634 | 9.2E-279 |
| 5 | g6778.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 341 | 634 | 9.2E-279 |
| 13 | g6778.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 50 | 67 | 7.8E-20 |
| 9 | g6778.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 126 | 137 | 3.1E-7 |
| 14 | g6778.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 126 | 137 | 7.8E-20 |
| 11 | g6778.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 171 | 187 | 7.8E-20 |
| 8 | g6778.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 177 | 185 | 3.1E-7 |
| 7 | g6778.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 209 | 228 | 3.1E-7 |
| 12 | g6778.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 209 | 228 | 7.8E-20 |
| 10 | g6778.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 230 | 247 | 7.8E-20 |
| 2 | g6778.t1 | Pfam | PF00106 | short chain dehydrogenase | 49 | 250 | 2.4E-35 |
| 1 | g6778.t1 | Pfam | PF00106 | short chain dehydrogenase | 358 | 559 | 9.3E-38 |
| 21 | g6778.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 22 | g6778.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 31 | - |
| 20 | g6778.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 32 | 640 | - |
| 16 | g6778.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 47 | 298 | 1.21E-62 |
| 17 | g6778.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 356 | 608 | 1.88E-62 |
| 15 | g6778.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
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 K11153 (retinol dehydrogenase 12)
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