General information for g7125.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinol dehydrogenase 13.
Parent gene
- The parent gene g7125 is located on chr_2: 21356954..21357907 (+ 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 | g7125 | g7125.t1 | TSS | g7125.t1 | 21356696 | 21356696 |
| chr_2 | g7125 | g7125.t1 | isoform | g7125.t1 | 21356774 | 21357907 |
| chr_2 | g7125 | g7125.t1 | exon | g7125.t1.exon1 | 21356774 | 21356853 |
| chr_2 | g7125 | g7125.t1 | cds | g7125.t1.CDS1 | 21356774 | 21356853 |
| chr_2 | g7125 | g7125.t1 | exon | g7125.t1.exon2 | 21356952 | 21357410 |
| chr_2 | g7125 | g7125.t1 | cds | g7125.t1.CDS2 | 21356952 | 21357410 |
| chr_2 | g7125 | g7125.t1 | exon | g7125.t1.exon3 | 21357469 | 21357907 |
| chr_2 | g7125 | g7125.t1 | cds | g7125.t1.CDS3 | 21357469 | 21357907 |
| chr_2 | g7125 | g7125.t1 | TTS | g7125.t1 | 21357983 | 21357983 |
Sequences
>g7125.t1 Gene=g7125 Length=978
ATGTTCTCAATATTAAAGAAAAAAAGTATTGTATGGAGCTCGACTATTATTGCTGGTTTG
GGCATTACATTTATCATTAAAGATTCAGTACAAGGAGAACGATTTAAAAAATCTATTGTT
GTAGATGGAAAAGTATTTATTGTTACTGGAGCTAACACAGGAATAGGCAAAGAAACTGCA
AAAAATCTTGCGAAAAGAAGAGGAATTGTTTATTTAGCATGTAGAGATTTACACAAATGC
GAAGCAGCAAGAAAAGAGATAATTCTGGCTACAAGAAATAAAAATGTCTTTTGTCGTGAA
CTTGATTTAGCTTCATTTAGTTCAATTAGAAGTTTTGTAAAGAGATTTAAATCAGAGCAA
AATCGTTTGGATGTTTTAATTAATAACGCAGGCGTTATGAGAATCCCACAAAAGCTTGTT
ACCCAAGAAGGATTCGAAATGCAGATTGGTACAAATCATTTAGGCCATTTTTTACTTACA
AATTTGTTATTAGATTATCTTAAAGCCTCTGCTCCTTCGCGAATTGTAACTGTATCAAGT
ATTGCTCATACACGTGGTGAAATAGATACAGCAGATTTCAATAGTGACAAAAATTATGAT
CCTAAGAAAGCTTATGAAATGTCAAAATTATGCAACGTACTCTTCACAAGACAGCTTGCA
AAAAAATTAGAAGGGACGGGAGTTACTTCGAACTGCTGTCATCCTGGTATAGTTGATACC
GAGTTAATGAGGCATATGGGCATAGTTAACTCATTTTTTGGAAAAATTTTTGTTTATCCC
TTTTTGTGGATTTTTACTAAAAAGGCAGAAGCTGGTGCTCAAACTGTTTTGTTTTGTGTA
CTTGAACCTGCGTTAAAAAATATTACTGGCGAATATTTCGCAGATTGTAAAAAGTCTGAA
ATGGCAGACCAAGCGAAAGATGATCAAATGGCAGAATGGTTGTGGCGCTTAAGTGAAAAA
TGGTGCCGATTAGCTTGA
>g7125.t1 Gene=g7125 Length=325
MFSILKKKSIVWSSTIIAGLGITFIIKDSVQGERFKKSIVVDGKVFIVTGANTGIGKETA
KNLAKRRGIVYLACRDLHKCEAARKEIILATRNKNVFCRELDLASFSSIRSFVKRFKSEQ
NRLDVLINNAGVMRIPQKLVTQEGFEMQIGTNHLGHFLLTNLLLDYLKASAPSRIVTVSS
IAHTRGEIDTADFNSDKNYDPKKAYEMSKLCNVLFTRQLAKKLEGTGVTSNCCHPGIVDT
ELMRHMGIVNSFFGKIFVYPFLWIFTKKAEAGAQTVLFCVLEPALKNITGEYFADCKKSE
MADQAKDDQMAEWLWRLSEKWCRLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g7125.t1 | Gene3D | G3DSA:3.40.50.720 | - | 36 | 324 | 1.0E-86 |
| 2 | g7125.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 12 | 323 | 7.3E-139 |
| 3 | g7125.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 12 | 323 | 7.3E-139 |
| 8 | g7125.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 45 | 62 | 3.4E-19 |
| 5 | g7125.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 121 | 132 | 5.7E-7 |
| 7 | g7125.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 121 | 132 | 3.4E-19 |
| 11 | g7125.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 167 | 183 | 3.4E-19 |
| 4 | g7125.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 173 | 181 | 5.7E-7 |
| 6 | g7125.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 205 | 224 | 5.7E-7 |
| 10 | g7125.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 205 | 224 | 3.4E-19 |
| 9 | g7125.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 226 | 243 | 3.4E-19 |
| 1 | g7125.t1 | Pfam | PF00106 | short chain dehydrogenase | 44 | 244 | 2.9E-32 |
| 15 | g7125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 8 | - |
| 17 | g7125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 26 | - |
| 16 | g7125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 325 | - |
| 13 | g7125.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 42 | 299 | 7.94E-58 |
| 12 | g7125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 26 | - |
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.
