General information for g9967.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 3-ketodihydrosphingosine reductase.
Parent gene
- The parent gene g9967 is located on chr_1: 6290898..6293445 (- 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_1 | g9967 | g9967.t1 | TTS | g9967.t1 | 6289701 | 6289701 |
| chr_1 | g9967 | g9967.t1 | isoform | g9967.t1 | 6289804 | 6290898 |
| chr_1 | g9967 | g9967.t1 | exon | g9967.t1.exon1 | 6289804 | 6290576 |
| chr_1 | g9967 | g9967.t1 | cds | g9967.t1.CDS1 | 6289804 | 6290576 |
| chr_1 | g9967 | g9967.t1 | exon | g9967.t1.exon2 | 6290643 | 6290756 |
| chr_1 | g9967 | g9967.t1 | cds | g9967.t1.CDS2 | 6290643 | 6290756 |
| chr_1 | g9967 | g9967.t1 | exon | g9967.t1.exon3 | 6290823 | 6290898 |
| chr_1 | g9967 | g9967.t1 | cds | g9967.t1.CDS3 | 6290823 | 6290898 |
| chr_1 | g9967 | g9967.t1 | TSS | g9967.t1 | 6291000 | 6291000 |
Sequences
>g9967.t1 Gene=g9967 Length=963
ATGATAATCATCTTGGTAATTTTCTTTCATATTATTATTTTTCAATGGCTTACACGAAAG
AAGAAAAATGTTGATGGAAAACACGTCGTTGTAACTGGTGGAAGTTCTGGCATCGGTCTA
TGGGTTGCAATAAATGCTGTTCGCAAAGGTGCTGATGTTACAATCGTTGCAAGAAACGTA
CGAATTTTAGAGAAAGCTGTTGCTGTCATTAAAGAAAACTGTATAAGAGATGATCAAAAA
GTGGAATATTATTCGTTAGATTTGTCAAAAGAGCATGAAATCATTGAAAAAGGATTTAAC
GACATTGAAGCAAAATTAGGTGATATTTATATGCTTGTGAACTGTGCTGGACAGGCATTA
TGCGGAGTAATTGAGGATGTGAAACCAGAAGATGCTCGATTTTTAATGAATCTAAATTAC
TTTGGAACTTTATACCCAATTCAATATGTTTTGCCCAAAATGAAAGTTAAAAAAGATGGT
ATCATTGTACTTACATCCTCACAAGCTGGTTTAATGGGAATTTATGGCTTGGGCCCTTAC
TCTGCTGCTAAGTTTGCTCTTCGTGGTTTGGCTGAAGCTCTTTCAATGGAAACAAAGCAT
TTAGGAATCAACGTGACTTTGGGATTACCTGCTGACACAGATACACCAGGATTTGCAAAT
GAACAAAAATCAAAGCCAAAAATTACACAAGAAATTTGTAGTGGTGGTGGTCTCTTTAAA
CCTGAAGATGTCGGAAAGAAACTTTTTGAAGATGCATTGAAAGGAAATTTCTTTTCAATT
TTAGGCTTTGAAAGTTGGATTTTATCAATTTTGTGCGTGGGAATGTCTCCCTGGAAAAAT
CCTCTTCTTGGTATTCTTCAATCTTATGTCATGGGCGCATTGAGAATGATAAGTTTTGTC
ATTCAATGGAATTTTGGAAGAATAGTCAAGAAATATTATCAACCAAAGGAAAAAACAAAT
TGA
>g9967.t1 Gene=g9967 Length=320
MIIILVIFFHIIIFQWLTRKKKNVDGKHVVVTGGSSGIGLWVAINAVRKGADVTIVARNV
RILEKAVAVIKENCIRDDQKVEYYSLDLSKEHEIIEKGFNDIEAKLGDIYMLVNCAGQAL
CGVIEDVKPEDARFLMNLNYFGTLYPIQYVLPKMKVKKDGIIVLTSSQAGLMGIYGLGPY
SAAKFALRGLAEALSMETKHLGINVTLGLPADTDTPGFANEQKSKPKITQEICSGGGLFK
PEDVGKKLFEDALKGNFFSILGFESWILSILCVGMSPWKNPLLGILQSYVMGALRMISFV
IQWNFGRIVKKYYQPKEKTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g9967.t1 | CDD | cd08939 | KDSR-like_SDR_c | 26 | 258 | 1.74222E-89 |
| 9 | g9967.t1 | Gene3D | G3DSA:3.40.50.720 | - | 17 | 265 | 1.5E-51 |
| 2 | g9967.t1 | PANTHER | PTHR43550 | 3-KETODIHYDROSPHINGOSINE REDUCTASE | 4 | 319 | 2.7E-105 |
| 3 | g9967.t1 | PANTHER | PTHR43550:SF3 | 3-KETODIHYDROSPHINGOSINE REDUCTASE | 4 | 319 | 2.7E-105 |
| 5 | g9967.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 28 | 45 | 2.7E-14 |
| 4 | g9967.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 107 | 118 | 2.7E-14 |
| 6 | g9967.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 154 | 170 | 2.7E-14 |
| 7 | g9967.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 180 | 199 | 2.7E-14 |
| 1 | g9967.t1 | Pfam | PF00106 | short chain dehydrogenase | 27 | 223 | 1.2E-42 |
| 11 | g9967.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 255 | - |
| 13 | g9967.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 256 | 276 | - |
| 12 | g9967.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 277 | 281 | - |
| 14 | g9967.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 282 | 301 | - |
| 10 | g9967.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 302 | 320 | - |
| 20 | g9967.t1 | ProSitePatterns | PS00061 | Short-chain dehydrogenases/reductases family signature. | 167 | 195 | - |
| 8 | g9967.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 22 | 283 | 1.97E-52 |
| 19 | g9967.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 2 | 19 | - |
| 17 | g9967.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 29 | 48 | - |
| 18 | g9967.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 256 | 278 | - |
| 16 | g9967.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 305 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04708 (3-dehydrosphinganine reductase)
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.
