General information for g3532.t23
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative D-beta-hydroxybutyrate dehydrogenase, mitochondrial.
Parent gene
- The parent gene g3532 is located on chr_3: 26225591..26228690 (- 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_3 | g3532 | g3532.t23 | TTS | g3532.t23 | 26221773 | 26221773 |
| chr_3 | g3532 | g3532.t23 | isoform | g3532.t23 | 26222052 | 26226624 |
| chr_3 | g3532 | g3532.t23 | exon | g3532.t23.exon1 | 26222052 | 26222723 |
| chr_3 | g3532 | g3532.t23 | cds | g3532.t23.CDS1 | 26222052 | 26222723 |
| chr_3 | g3532 | g3532.t23 | exon | g3532.t23.exon2 | 26222785 | 26222982 |
| chr_3 | g3532 | g3532.t23 | cds | g3532.t23.CDS2 | 26222785 | 26222982 |
| chr_3 | g3532 | g3532.t23 | exon | g3532.t23.exon3 | 26225543 | 26225806 |
| chr_3 | g3532 | g3532.t23 | cds | g3532.t23.CDS3 | 26225543 | 26225806 |
| chr_3 | g3532 | g3532.t23 | exon | g3532.t23.exon4 | 26226033 | 26226264 |
| chr_3 | g3532 | g3532.t23 | cds | g3532.t23.CDS4 | 26226033 | 26226038 |
| chr_3 | g3532 | g3532.t23 | exon | g3532.t23.exon5 | 26226546 | 26226624 |
| chr_3 | g3532 | g3532.t23 | TSS | g3532.t23 | 26226624 | 26226624 |
Sequences
>g3532.t23 Gene=g3532 Length=1445
AGTAGGTTTTTAAATTTTGAGTCGAGCGGTTCTTTAAAACCATAACTCGCAAAAGCCGAA
GAAAATAAATAGTGACAGACATCATACTCTACTCTATAAAAATAATTTACTTTTTCGCTG
TGGATAAGCAGAGAAAAGAAAGAAATTTTTTTTTGGAAAATTTCAAAGAGAAGAAAATAA
ATTGAACTCGTAAATAATAATAAGAATAAGAGTGAAATTGGCTCATCGCGTGTGTGTATT
TTATTTTTGAACCCTGTCTGTGGAAAAAAGCTATTCGCTCAGTGTAAAATTAACTGACCG
GCGAAATGCAGGTCCCAAGACTAGAAAGACGTCGTGCTTCATTGCGCCATGAGTCATTGA
GACGTGGCAGCATCGTTCAACCCATTTCTAAAGAGGTGCCATGGGATATTTTTGATAGAT
TATTCCTGCCAGTACTTTACTGTCATGCTATCGCCATCATTTTTAGTGCTGTCTTGCAAG
TTTTTGAAATTCAATTTGCCTTCTCAACATTTGGAATTTTTATACTCCTTTCAATAGCTA
CCGTCACGCTTACACTCTTCTATCACAATCTTAAGGCATCTGGAAAAGCAGTTTTAGTAA
CCGGCTGTGAAAATCCACTCGCTTGGTATTTATGCAAGAAACTCGATGAAATTGGTTTTT
CCGTTTTTGCTGGATTCAAGAATGTTGCCGATAATTCTGATGCTGAACTTCTTACTGAAG
AATGCTCTGCTCGTGTACGACTTGTTCAAATTGATGCTTCATCTGATACTCAGATGCAAG
AAGCTGCAAAGTTTATTGAAAACAATTTGCCTGATGGTGCAACTGGTTTATGGGCATTAT
TGCATTGCGATCATTGGAATGCAATTGGTGAACTCGAATGGATTCCTCCAGCTGTCTTGA
AAAAATCCTTGGAAACTAATGTTGCTGGAACCGTACGCATTACTCAAATCTTTTTGCCAA
TCATTCGTCGTGGCAAGGGACGTGTTGTTTATCTTTCATCAGCAATGTCAAAGATCTACA
ACCCAGTGCGTGGCATTCAAACAGCTATTAATAATGCTATTGAGAGCTTGGCTCTATGTC
TCCGTTCAGAAATGAGACGTCATGGTGTTCATGTTATTGTAGTTGCTGCAGGAGAATTTG
CTTCAGGCACCGCGTGGTTAGATAATGAAGATCTTTGTGAACAGGCAAAACTTATGTGGA
AAAATATGAATGATTCATTAAGATTTGAAATTGTCGATGAAAAATATTTCGAGTTCACTA
TTCGTCAATTGGAACGTTATACAAAAGTTACTGTTGATTTAACACCCGCCATTCATACAC
TCATCGATGCCGTTCAAAAAGCTTTTCCTTTGCCACGATACACTCCCATTACTTTCGAGG
AAAAACTCAAGACACTTATTGCCGATTACATGCCTTATGCTGTTTATGATGTTATCTACA
ATTAA
>g3532.t23 Gene=g3532 Length=379
MQVPRLERRRASLRHESLRRGSIVQPISKEVPWDIFDRLFLPVLYCHAIAIIFSAVLQVF
EIQFAFSTFGIFILLSIATVTLTLFYHNLKASGKAVLVTGCENPLAWYLCKKLDEIGFSV
FAGFKNVADNSDAELLTEECSARVRLVQIDASSDTQMQEAAKFIENNLPDGATGLWALLH
CDHWNAIGELEWIPPAVLKKSLETNVAGTVRITQIFLPIIRRGKGRVVYLSSAMSKIYNP
VRGIQTAINNAIESLALCLRSEMRRHGVHVIVVAAGEFASGTAWLDNEDLCEQAKLMWKN
MNDSLRFEIVDEKYFEFTIRQLERYTKVTVDLTPAIHTLIDAVQKAFPLPRYTPITFEEK
LKTLIADYMPYAVYDVIYN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3532.t23 | Gene3D | G3DSA:3.40.50.720 | - | 93 | 370 | 5.4E-32 |
| 2 | g3532.t23 | PANTHER | PTHR43313:SF36 | GH26015P | 34 | 379 | 1.1E-93 |
| 3 | g3532.t23 | PANTHER | PTHR43313 | SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY 9C | 34 | 379 | 1.1E-93 |
| 1 | g3532.t23 | Pfam | PF00106 | short chain dehydrogenase | 94 | 284 | 3.9E-19 |
| 9 | g3532.t23 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 38 | - |
| 12 | g3532.t23 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 39 | 60 | - |
| 10 | g3532.t23 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 61 | 65 | - |
| 11 | g3532.t23 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 86 | - |
| 8 | g3532.t23 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 87 | 379 | - |
| 6 | g3532.t23 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 90 | 286 | 4.14E-29 |
| 5 | g3532.t23 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 38 | 60 | - |
| 4 | g3532.t23 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 64 | 86 | - |
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. There were no conditions that were differentially expressed