General information for g9378.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sorbitol dehydrogenase.
Parent gene
- The parent gene g9378 is located on chr_1: 2304981..2306104 (- 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 | g9378 | g9378.t3 | TTS | g9378.t3 | 2304155 | 2304155 |
| chr_1 | g9378 | g9378.t3 | isoform | g9378.t3 | 2304206 | 2306104 |
| chr_1 | g9378 | g9378.t3 | exon | g9378.t3.exon1 | 2304206 | 2304888 |
| chr_1 | g9378 | g9378.t3 | cds | g9378.t3.CDS1 | 2304617 | 2304888 |
| chr_1 | g9378 | g9378.t3 | exon | g9378.t3.exon2 | 2304954 | 2305226 |
| chr_1 | g9378 | g9378.t3 | cds | g9378.t3.CDS2 | 2304954 | 2305226 |
| chr_1 | g9378 | g9378.t3 | exon | g9378.t3.exon3 | 2305293 | 2305745 |
| chr_1 | g9378 | g9378.t3 | cds | g9378.t3.CDS3 | 2305293 | 2305745 |
| chr_1 | g9378 | g9378.t3 | exon | g9378.t3.exon4 | 2305799 | 2305950 |
| chr_1 | g9378 | g9378.t3 | cds | g9378.t3.CDS4 | 2305799 | 2305886 |
| chr_1 | g9378 | g9378.t3 | exon | g9378.t3.exon5 | 2305996 | 2306104 |
| chr_1 | g9378 | g9378.t3 | TSS | g9378.t3 | 2306154 | 2306154 |
Sequences
>g9378.t3 Gene=g9378 Length=1670
GCTTATCAATTTAGCTTTCGTCAAGTGTGCATCTTCAAATATAATCACTTATTTATTTTT
ACAAAACAAATTTATTATTGCACAATCTCTCTCTCTCACATGTGTGTAACAATCATTTGC
TCGCGAGTCTCGTGATAATAAACAAGTACTAAATCTATAAATAAAATACAAAAATGGCTT
CAAATAATTTAACTGCTGTGCTTTATGGAGTTGAAGATTTGCGATTAGAAAATCAAGAAA
TTCCTGAAATTAAAGATGATGAGGTATTAATCGAGATGGATTGCGTTGGAATTTGTGGAA
GTGATGTACATTATTTAGTTCATGGTCGAATTGGTGACTTCATTCTAAAAGATAAGATGA
TAATTGGTCATGAAAGTAGCGGAGTTGTAAGAAAACTTGGAAAAAATGTGAAGAATCTGC
AAGTTAATGATAGAGTTGCAATCGAACCAGGTGTCGCTTGTCGTTTATGTGATTATTGCA
AGACTGGGAAATATAATTTGTGTCCCGAGATGAAATTTTGTGCAACACCACCGTACGATG
GAAACCTGAGAAAATTTTATGCACATGCAGCTGATTTTTGTTTCAAATTACCTGATCATG
TTACAATGGAAGAGGCCGCTCTCTTAGAACCGTTAAGTGTGGGTGTTCATGCTTGTCGAC
GTGCACAAGTAAGCTTAGGTGACAACTTATTGATTTTAGGCAGTGGTCCAATTGGCCTTG
TAACATTGATATGTGCAAAAGAAATGGGAGCAAGTAAAGTCATAATCACTGACCTGCTTC
AATCCAGACTTGATGTTGCCAAAGAATTGGGTGCAGACTATACACTTCTTGTTAATAAAA
ATGATACAGAAAAAGAACTTGTAAAGAAAATTCATAATTTGCTTGGTAATGTTGCGCCAA
ATAAATCAATCGATTGTAGTGGATTTGAAGCAACTAATCGATTAGGTCTTGCAGCAACTG
CTAGTGGTGGATGTTTTGTAATAGTAGGATGTGGACCACCTGAAGTAAAATTAGAATTAA
TGAGCGCATTGACCTGTGAAGTTGACATTCGCGGTGTATTTAGATATGCAAATGATTATC
AAGCAGCACTTGCACTTGTGGCTACAGGAAAAGTCAATGTCAAAAAACTTATCACACATC
ATTTTGATATCACTGAGACACTTGATGCCTTCGATACATCACGTTATGGTAAAGAGAATG
CAATTAAAGTTATGATTCATTGTCAGCCACGAAACAAAAATAATCCAAAACCTTTTTAAT
TTTTTTGGACTCATTGCTTTCAAGTACTATAAATCATTCCTGCGGCCAGTAAACGAAGGG
AGGAGAATGAGCCAATAAAAAAATTATTTTATTCCTGAATCCTTTTTGATCATAAATTTA
AAATTTTTTTTATTCATCTTTTCCCCTTTTATACGATATCATATTTACTCCTCTCTACAA
TCGAATGAGAATTTTTATTTGCATTTTTTTGAAGCCATAAAAATCCACTTGAATTTTACA
CATCCACTCCATTCATCGCATGCTGCGTTTTTTGCCTAGCCATGGGCTTCCTACAGATCG
TCCTTTCATCTTTCATTTCCCGTTCGTTCGCTTTTTTTGCTATGACCGTGTTTTGGACGA
AAAGAAGAAATGAACGAGATCCTTTTTTTACTGAATTGTTTTTTTTTATT
>g9378.t3 Gene=g9378 Length=361
MASNNLTAVLYGVEDLRLENQEIPEIKDDEVLIEMDCVGICGSDVHYLVHGRIGDFILKD
KMIIGHESSGVVRKLGKNVKNLQVNDRVAIEPGVACRLCDYCKTGKYNLCPEMKFCATPP
YDGNLRKFYAHAADFCFKLPDHVTMEEAALLEPLSVGVHACRRAQVSLGDNLLILGSGPI
GLVTLICAKEMGASKVIITDLLQSRLDVAKELGADYTLLVNKNDTEKELVKKIHNLLGNV
APNKSIDCSGFEATNRLGLAATASGGCFVIVGCGPPEVKLELMSALTCEVDIRGVFRYAN
DYQAALALVATGKVNVKKLITHHFDITETLDAFDTSRYGKENAIKVMIHCQPRNKNNPKP
F
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g9378.t3 | CDD | cd05285 | sorbitol_DH | 8 | 350 | 0.0 |
| 9 | g9378.t3 | Gene3D | G3DSA:3.90.180.10 | - | 13 | 335 | 2.8E-115 |
| 8 | g9378.t3 | Gene3D | G3DSA:3.40.50.720 | - | 156 | 296 | 2.8E-115 |
| 3 | g9378.t3 | PANTHER | PTHR43161 | SORBITOL DEHYDROGENASE | 4 | 348 | 2.7E-141 |
| 2 | g9378.t3 | Pfam | PF08240 | Alcohol dehydrogenase GroES-like domain | 29 | 138 | 8.7E-27 |
| 1 | g9378.t3 | Pfam | PF00107 | Zinc-binding dehydrogenase | 179 | 310 | 1.4E-21 |
| 7 | g9378.t3 | ProSitePatterns | PS00059 | Zinc-containing alcohol dehydrogenases signature. | 65 | 79 | - |
| 6 | g9378.t3 | SMART | SM00829 | PKS_ER_names_mod | 12 | 344 | 2.7E-4 |
| 5 | g9378.t3 | SUPERFAMILY | SSF50129 | GroES-like | 7 | 175 | 5.53E-55 |
| 4 | g9378.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 143 | 314 | 8.02E-35 |
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:0008270 | zinc ion binding | MF |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00008 (L-iditol 2-dehydrogenase)
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.
