General information for g719.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 3-hydroxy-3-methylglutaryl-coenzyme A reductase.
Parent gene
- The parent gene g719 is located on chr_3: 5497027..5501085 (- 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 | g719 | g719.t1 | TTS | g719.t1 | 5489431 | 5489431 |
| chr_3 | g719 | g719.t1 | isoform | g719.t1 | 5490150 | 5497357 |
| chr_3 | g719 | g719.t1 | exon | g719.t1.exon1 | 5490150 | 5490219 |
| chr_3 | g719 | g719.t1 | cds | g719.t1.CDS1 | 5490150 | 5490219 |
| chr_3 | g719 | g719.t1 | exon | g719.t1.exon2 | 5490282 | 5492466 |
| chr_3 | g719 | g719.t1 | cds | g719.t1.CDS2 | 5490282 | 5492466 |
| chr_3 | g719 | g719.t1 | exon | g719.t1.exon3 | 5492531 | 5492673 |
| chr_3 | g719 | g719.t1 | cds | g719.t1.CDS3 | 5492531 | 5492673 |
| chr_3 | g719 | g719.t1 | exon | g719.t1.exon4 | 5492734 | 5492821 |
| chr_3 | g719 | g719.t1 | cds | g719.t1.CDS4 | 5492734 | 5492821 |
| chr_3 | g719 | g719.t1 | exon | g719.t1.exon5 | 5497030 | 5497357 |
| chr_3 | g719 | g719.t1 | cds | g719.t1.CDS5 | 5497030 | 5497357 |
| chr_3 | g719 | g719.t1 | TSS | g719.t1 | NA | NA |
Sequences
>g719.t1 Gene=g719 Length=2814
ATGGTGAAAACTGGACATTTATTTCGAGCGCATGGAGAATTTTGTGCATCGCATCCATGG
GAGGTGATAGTGGCATTGATAACTTTTACTGCCTGTATGTTTAGTGTTGACAAAGGAAGC
AGTTCTGCAAATGATCCGCTAATTAATCCCACAATAAAACCTATTCAAATGAGACAGTGT
CATGGATGGCGAGAGTCTTGTGATGGCTTCGAAGCTCAATATATTGCAGCAGACGTAATT
TTGATGACAATTGTAAGATGTTCAGCAGTTCTTTATTGCTATTATCAATTCTACAATCTC
CATAAATTGGGATCAAAATATATTCTTGGTATTGCTGGTCTTTTTACCGTTTTTTCAAGC
TTCATATTTACATCAAGCATTATGAACTTTTTGGAAAGTGACATATCAGATTTAAAGGAT
GCATTATTCTTTTTCCTTTTACTCATTGACTTGTCAAAAGCTGGTATTCTTGCAAAATTG
GCATTAAGTGGTTCAAACTCACAAGAAGTTACACAAAACATAGCACGCGGAATGGAAATT
CTCGGACCAGCTATTTCATTGGATACAATGGTTGAAGCTTTGGTGATTGGTGTTGGAACG
CTCTCTGGTGTACAGAGACTAGAAGTTTTAAGTGGATTTGCCGTCATGTCTGTAATCGTG
AATTATGTTGTGTTCATGACGTTTTATCCAGCTTGTTTATCATTAACACTTGATTTATCG
CGTAATTGCAGCGGAAATAAAGCCGTTGCAGTAAATGCTAATACTGAAACAACAGAGAAG
CAAAAGATTCGTGATCCATCGCTTATTCGAGCCTTAAGTGAAGAAGATCAGAAACAAAAT
CCAATCATACAGCGTGTTAAGCTTATTATGTCAAGCGGTCTTATGATTGTTCATGCACAT
AGTCGTCTTACATTTTCTGATAATGATGACGTAGAAGATTCTCATGTCAATGTCAACACA
AACCCTGGCGCTGACGTAAAGAATCTAAATATGGCTCAACAAATGAACAAAACAGAGTCG
AGTGACATTTCTGACTATATCATGAGATGGTTATCAATTAGTACAGAACAGATATTCATT
CTTATTCTATTAGTAGCACTTTGTATTAAATTTATTTTCTTCGATCGTGACGATCTCACT
AATCAAATTCAGCGCGATTTGGCAAAACAAATTGAAGATGAAGAGAGAAGAAAACGTGAG
CAGGAATTAGAAAATCAAATGAGAAAAGAAATTATTGCAAAAGTGCCACCTACACCCACC
ATACAACTATCATCACGCGATCCATCACCACCTTTACAACGTCGTGCATTATTTTCAATT
CACGAGGAGGATCCATTGATGAAAGAAGCTGAAGTTCAAACTGACCTCACTGCCTTTGAT
GTTTTTGGCGACTCTGATGAAGATAATCCCGAATTTATTGAGTCTGCTCTTGTGCCAGTA
CGCCCACCGCGATCAATTGATGAATGTGTAAAAATTATGATGTCAGATGAAGGTGCCAAA
TCATTAACTGATGAAGAACTCATAAATTTAGTAAATGCTGGTGGAAATTATTTGCCATTA
CATAAGATTGAAACAATCATTGAAGATGCAGAGCGTGGAGTCAAAATTCGACGTCAAATT
ATTGCCTCTCGTATGGGCTATAAAAATGGAAATGATATTTTTGGAAGCTTGAGCTACCGC
ACGTATGATTATAGTAAAGTGATGAATGCATGTTGCGAAAATGTCCTTGGATATGTTGAA
ATTCCAGTTGGTTACGCTGGTCCCTTGGTGCTCGATAATAAAAAATATTTCGTTCCAATG
GCAACAACTGAGGGAGCTCTTGTTGCTTCAACAAATCGTGGTTGCAAAGCTCTATCATAT
TATGGTGTTCGTAGTATTGTTGAAGATGTTGGTATGACAAGAGCACCATGTGTTAAATTT
CCAGATGTCGTAAGTGCTGCTCAAGCTAAACGATGGATGGAAACTGCCGAAAATTTCACT
ACAATTAAACAGGCCTTCGATTCAACTAGTCGATTTGCACGCTTACAAGAACTTTTAATT
TCAATTGATGGTCCACAATTATATATTCGCTTTAGAGCATTCACAGGTGATGCAATGGGA
ATGAATATGGTTTCAAAAGGTGCTGAAAATGCTTTAAGAATTGTACAACATAATTTCCCA
GAAATGCAAATCATTAGTTTAAGTGGAAACTTTTGTTCAGATAAAAAGCCTGCTGCAATC
AATTGGATTAAAGGTCGTGGTAAACGAGTTGTTTGTGAGTCACGTATTAGTGAAGAAGTG
CTTAAGAATTTGTTAAAAACCGATGCAAAGACATTAGTGCAATGTAATAAATTGAAAAAT
ATGGCGGGTTCTGCAATGGCGGGAAGTATTGGTGGCAATAATGCACATGCAGCCAACATG
GTCACAGCAATTTTCATAGCAACAGGCCAAGATCCAGCACAGAATATTACTAGTAGCAAT
TGCTCTACAAATATGGAGCTTCATAGTGAAAATCCAAATGATTTATATATCACATGCACA
ATGCCTTCATTTGAGGTCGGAACAGTTGGTGGTGGAACAGTTTTACCCGGACAAAGTGCT
TGCTTAGAAGTTCTCGGCGTTAAAGGTGCTCATCAGTCACATCCTGCAGAGAATAGTAAA
CAACTAGCTCGTATCATTTGCGCAACAGTTATGGCCGGTGAACTTTCACTTATGGCAGCC
TTAGTCAATAGTGATCTAGTCAAAAGTCACATGAAACACAATAGATCTTCCGTGGTTGTC
AATTCATTTTCTACCTCAAATCGAGCATCATCGGCCTCAATTCCAAAAATTTAA
>g719.t1 Gene=g719 Length=937
MVKTGHLFRAHGEFCASHPWEVIVALITFTACMFSVDKGSSSANDPLINPTIKPIQMRQC
HGWRESCDGFEAQYIAADVILMTIVRCSAVLYCYYQFYNLHKLGSKYILGIAGLFTVFSS
FIFTSSIMNFLESDISDLKDALFFFLLLIDLSKAGILAKLALSGSNSQEVTQNIARGMEI
LGPAISLDTMVEALVIGVGTLSGVQRLEVLSGFAVMSVIVNYVVFMTFYPACLSLTLDLS
RNCSGNKAVAVNANTETTEKQKIRDPSLIRALSEEDQKQNPIIQRVKLIMSSGLMIVHAH
SRLTFSDNDDVEDSHVNVNTNPGADVKNLNMAQQMNKTESSDISDYIMRWLSISTEQIFI
LILLVALCIKFIFFDRDDLTNQIQRDLAKQIEDEERRKREQELENQMRKEIIAKVPPTPT
IQLSSRDPSPPLQRRALFSIHEEDPLMKEAEVQTDLTAFDVFGDSDEDNPEFIESALVPV
RPPRSIDECVKIMMSDEGAKSLTDEELINLVNAGGNYLPLHKIETIIEDAERGVKIRRQI
IASRMGYKNGNDIFGSLSYRTYDYSKVMNACCENVLGYVEIPVGYAGPLVLDNKKYFVPM
ATTEGALVASTNRGCKALSYYGVRSIVEDVGMTRAPCVKFPDVVSAAQAKRWMETAENFT
TIKQAFDSTSRFARLQELLISIDGPQLYIRFRAFTGDAMGMNMVSKGAENALRIVQHNFP
EMQIISLSGNFCSDKKPAAINWIKGRGKRVVCESRISEEVLKNLLKTDAKTLVQCNKLKN
MAGSAMAGSIGGNNAHAANMVTAIFIATGQDPAQNITSSNCSTNMELHSENPNDLYITCT
MPSFEVGTVGGGTVLPGQSACLEVLGVKGAHQSHPAENSKQLARIICATVMAGELSLMAA
LVNSDLVKSHMKHNRSSVVVNSFSTSNRASSASIPKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 33 | g719.t1 | CDD | cd00643 | HMG-CoA_reductase_classI | 505 | 915 | 0.0 |
| 15 | g719.t1 | Coils | Coil | Coil | 384 | 409 | - |
| 13 | g719.t1 | Gene3D | G3DSA:1.10.3270.10 | HMGR | 490 | 581 | 2.3E-23 |
| 14 | g719.t1 | Gene3D | G3DSA:3.90.770.10 | - | 582 | 901 | 2.8E-140 |
| 12 | g719.t1 | Gene3D | G3DSA:3.30.70.420 | - | 631 | 747 | 2.8E-140 |
| 3 | g719.t1 | PANTHER | PTHR10572 | 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE | 216 | 920 | 1.9E-187 |
| 9 | g719.t1 | PRINTS | PR00071 | Hydroxymethylglutaryl-coenzyme A reductase signature | 571 | 592 | 5.9E-80 |
| 7 | g719.t1 | PRINTS | PR00071 | Hydroxymethylglutaryl-coenzyme A reductase signature | 598 | 618 | 5.9E-80 |
| 4 | g719.t1 | PRINTS | PR00071 | Hydroxymethylglutaryl-coenzyme A reductase signature | 688 | 706 | 5.9E-80 |
| 8 | g719.t1 | PRINTS | PR00071 | Hydroxymethylglutaryl-coenzyme A reductase signature | 728 | 753 | 5.9E-80 |
| 5 | g719.t1 | PRINTS | PR00071 | Hydroxymethylglutaryl-coenzyme A reductase signature | 779 | 805 | 5.9E-80 |
| 6 | g719.t1 | PRINTS | PR00071 | Hydroxymethylglutaryl-coenzyme A reductase signature | 834 | 855 | 5.9E-80 |
| 1 | g719.t1 | Pfam | PF12349 | Sterol-sensing domain of SREBP cleavage-activation | 104 | 237 | 7.6E-16 |
| 2 | g719.t1 | Pfam | PF00368 | Hydroxymethylglutaryl-coenzyme A reductase | 534 | 915 | 1.4E-132 |
| 18 | g719.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 19 | - |
| 29 | g719.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 36 | - |
| 23 | g719.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 37 | 73 | - |
| 25 | g719.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 95 | - |
| 20 | g719.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 96 | 106 | - |
| 27 | g719.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 107 | 130 | - |
| 24 | g719.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 131 | 141 | - |
| 32 | g719.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 162 | - |
| 16 | g719.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 163 | 182 | - |
| 31 | g719.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 183 | 204 | - |
| 21 | g719.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 205 | 209 | - |
| 30 | g719.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 232 | - |
| 17 | g719.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 233 | 357 | - |
| 28 | g719.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 358 | 374 | - |
| 22 | g719.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 375 | 881 | - |
| 26 | g719.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 882 | 902 | - |
| 19 | g719.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 903 | 937 | - |
| 40 | g719.t1 | ProSitePatterns | PS00066 | Hydroxymethylglutaryl-coenzyme A reductases signature 1. | 690 | 704 | - |
| 39 | g719.t1 | ProSitePatterns | PS00318 | Hydroxymethylglutaryl-coenzyme A reductases signature 2. | 846 | 853 | - |
| 41 | g719.t1 | ProSitePatterns | PS01192 | Hydroxymethylglutaryl-coenzyme A reductases signature 3. | 900 | 913 | - |
| 46 | g719.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 32 | 5.0 |
| 44 | g719.t1 | ProSiteProfiles | PS50156 | Sterol-sensing domain (SSD) profile. | 78 | 235 | 36.612 |
| 45 | g719.t1 | ProSiteProfiles | PS50065 | Hydroxymethylglutaryl-coenzyme A reductases family profile. | 504 | 915 | 116.48 |
| 11 | g719.t1 | SUPERFAMILY | SSF56542 | Substrate-binding domain of HMG-CoA reductase | 484 | 904 | 4.84E-99 |
| 10 | g719.t1 | SUPERFAMILY | SSF55035 | NAD-binding domain of HMG-CoA reductase | 631 | 747 | 5.23E-45 |
| 42 | g719.t1 | TIGRFAM | TIGR00920 | 2A060605: 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 5 | 927 | 0.0 |
| 43 | g719.t1 | TIGRFAM | TIGR00533 | HMG_CoA_R_NADP: hydroxymethylglutaryl-CoA reductase (NADPH) | 508 | 915 | 7.0E-141 |
| 35 | g719.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 79 | 98 | - |
| 38 | g719.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 108 | 130 | - |
| 37 | g719.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 143 | 165 | - |
| 34 | g719.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 180 | 202 | - |
| 36 | g719.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 209 | 231 | - |
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:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | MF |
| GO:0015936 | coenzyme A metabolic process | BP |
| GO:0055114 | NA | NA |
| GO:0050661 | NADP binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0004420 | hydroxymethylglutaryl-CoA reductase (NADPH) activity | MF |
| GO:0005789 | endoplasmic reticulum membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K00021 (hydroxymethylglutaryl-CoA reductase (NADPH))
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.
