General information for g3690.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Hydroxymethylglutaryl-CoA synthase 1.
Parent gene
- The parent gene g3690 is located on chr_3: 27442852..27444228 (+ 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 | g3690 | g3690.t1 | TSS | g3690.t1 | 27442282 | 27442282 |
| chr_3 | g3690 | g3690.t1 | isoform | g3690.t1 | 27442852 | 27444228 |
| chr_3 | g3690 | g3690.t1 | exon | g3690.t1.exon1 | 27442852 | 27444228 |
| chr_3 | g3690 | g3690.t1 | cds | g3690.t1.CDS1 | 27442852 | 27444228 |
| chr_3 | g3690 | g3690.t1 | TTS | g3690.t1 | NA | NA |
Sequences
>g3690.t1 Gene=g3690 Length=1377
ATGTCGTGGCCACAAAATGTCGGTATATTAGGAATTGAGTTAGTTTTTCCATCACTTTTT
GTTGATCAAAGTGAGTTAGAAAAATACGATGGTGTTGCTGAAGGAAAGTATGTAATTGGT
TTAGGACAAAGTAGAATGGGATTTTGCACAGACCGTGAAGACATCAACTCACTTTGTCTG
ACTGTTGTTAGTAATTTAATGAAACGCTACAATATTGAGCCAAAAAATATTGGTAGATTA
GAAGTAGGAACTGAGACAATAATTGATAAATCAAAATCAGTTAAGTCGGTGTTGATGCAG
CTTTTTGAACCATATGGTGCTTGTGATTTGGAAGGAATAGATACTACAAATGCGTGCTAT
GGAGGAACTGCTGCTCTTTTCAATGCTATCAATTGGGTTGAATCGTCAAGTTATGATGGA
CGTTTAGCTCTTGTTGTTTGTGGTGATATTGCTGTTTATGCAAAAGGATCAGCACGACCA
ACAGGTGGTGCCGGAGCCATTGCTTTATTGGTCGGTCCAGATGCACCACTTGTATTAGAT
CGTAAAGTTAGATCAACATACATGAAACATGCTTATGATTTCTATAAGCCAGATTTGACA
TCAGAATTTCCAATAGTGGATGGCAAACTTTCAATACAATGCTACTTAAGTGCATTAGAC
AATTGTTACAAATTATATTGTGAAAAATATCAGCGACATCATCCTGAAAATAAAGTCGTC
GGATTAAATCATTTTGATGCTTTAATTTTTCACACTCCATATTGCAAACTCGTACAAAAA
TCATTGGCACGCATCAGCTTGAACGATTTTCTCTTAACAACAGACCCACAGCAGCGAAAG
GAAACATATCCATCATTCCATGAAAAGTATGATACGATAAAACTCGAGGACACTTATTTT
GACCGTGATGTCGAAAAAATCTTTATGGACTATTCCAAGGAGACTTTCAATCAAAAAACT
AAACCATCGCTCTTCCTTGCCAATCAGGTAGGTAATATGTATACACCATCAGTCTATTCT
GGCCTAGTCTCGTTGCTCGTAAGCGTAGATGGTGACGTTAACAAACTTCTTGGTAGACAT
GTTGGCGTTTTTTCATATGGATCTGGATTAGCTTCAACAATGTATTCAATCAGTATAACA
AATGATACCGAAAAATTACAAGCGCTTCTAGATAAACTTTCATATGTTAAACCATTACTT
GAACAGAGAACTAAAATTTCACCTCAAGAATTTACAGAATTAATGGAAATACGTGTTCAA
AATTCACACCGTACTAAATATGAACCGAGTGGAGCGATTGAGAGACTTTTTCCGGGTACT
TATTATTTAAAGTATGTTGATGAGATGCATCGACGAACATACGAAAAACGCGAATAA
>g3690.t1 Gene=g3690 Length=458
MSWPQNVGILGIELVFPSLFVDQSELEKYDGVAEGKYVIGLGQSRMGFCTDREDINSLCL
TVVSNLMKRYNIEPKNIGRLEVGTETIIDKSKSVKSVLMQLFEPYGACDLEGIDTTNACY
GGTAALFNAINWVESSSYDGRLALVVCGDIAVYAKGSARPTGGAGAIALLVGPDAPLVLD
RKVRSTYMKHAYDFYKPDLTSEFPIVDGKLSIQCYLSALDNCYKLYCEKYQRHHPENKVV
GLNHFDALIFHTPYCKLVQKSLARISLNDFLLTTDPQQRKETYPSFHEKYDTIKLEDTYF
DRDVEKIFMDYSKETFNQKTKPSLFLANQVGNMYTPSVYSGLVSLLVSVDGDVNKLLGRH
VGVFSYGSGLASTMYSISITNDTEKLQALLDKLSYVKPLLEQRTKISPQEFTELMEIRVQ
NSHRTKYEPSGAIERLFPGTYYLKYVDEMHRRTYEKRE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3690.t1 | CDD | cd00827 | init_cond_enzymes | 6 | 377 | 0 |
| 6 | g3690.t1 | Gene3D | G3DSA:3.40.47.10 | - | 2 | 458 | 0 |
| 3 | g3690.t1 | PANTHER | PTHR43323 | 3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE | 6 | 457 | 0 |
| 1 | g3690.t1 | Pfam | PF01154 | Hydroxymethylglutaryl-coenzyme A synthase N terminal | 3 | 176 | 0 |
| 2 | g3690.t1 | Pfam | PF08540 | Hydroxymethylglutaryl-coenzyme A synthase C terminal | 177 | 457 | 0 |
| 4 | g3690.t1 | SUPERFAMILY | SSF53901 | Thiolase-like | 6 | 174 | 0 |
| 5 | g3690.t1 | SUPERFAMILY | SSF53901 | Thiolase-like | 177 | 455 | 0 |
| 7 | g3690.t1 | TIGRFAM | TIGR01833 | HMG-CoA-S_euk: hydroxymethylglutaryl-CoA synthase | 3 | 457 | 0 |
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:0008299 | isoprenoid biosynthetic process | BP |
| GO:0010142 | farnesyl diphosphate biosynthetic process, mevalonate pathway | BP |
| GO:0004421 | hydroxymethylglutaryl-CoA synthase activity | MF |
| GO:0016746 | acyltransferase activity | MF |
| GO:0006084 | acetyl-CoA metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K01641 (hydroxymethylglutaryl-CoA synthase)
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.
