Gene loci information

Transcript annotation

  • This transcript has been annotated as 3-hydroxy-3-methylglutaryl-coenzyme A reductase.

Parent gene

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.t4 isoform g719.t4 5491960 5501085
chr_3 g719 g719.t4 exon g719.t4.exon1 5491960 5492466
chr_3 g719 g719.t4 cds g719.t4.CDS1 5491961 5492466
chr_3 g719 g719.t4 exon g719.t4.exon2 5492531 5492673
chr_3 g719 g719.t4 cds g719.t4.CDS2 5492531 5492673
chr_3 g719 g719.t4 exon g719.t4.exon3 5492734 5492821
chr_3 g719 g719.t4 cds g719.t4.CDS3 5492734 5492821
chr_3 g719 g719.t4 exon g719.t4.exon4 5497030 5497468
chr_3 g719 g719.t4 cds g719.t4.CDS4 5497030 5497357
chr_3 g719 g719.t4 exon g719.t4.exon5 5500772 5501085
chr_3 g719 g719.t4 TSS g719.t4 5501096 5501096
chr_3 g719 g719.t4 TTS g719.t4 NA NA

Sequences

>g719.t4 Gene=g719 Length=1491
TTTTTCTTCTCTTTCATCTAAAATAGATGTTTTAAGACATGTTGCTGCTGATTTTCTCTA
GTACTTATAAAACAGAACATGCCAAATATTGAAATGAAACATCAGCACAAGTGAATTAAA
TAATAGAAAAAGTGACAAAAGTTACATAAAATATAATTGTATAAGAATAGAGAAGAATTC
CTATATGAAAGTGTGAAAGTGAAAAAGAAAAATTCGTGAAAATTCTATCTTATCTCTTGA
ATAAAAAAATTTTGACTTGTGCAAAAAATCTGTTAATAAATAAAGTCAATTAAAATATAA
AGCGACAAGTACAGAGGAAAAAACTTCATTCATCGATTAAAAATTAATCAACAATACTGC
TTAGTGTTACTACTTTAAATTAATTACTTCAACGTCAAAACTTGTTAATAAATCTATAAA
TCAAAATGGTGAAAACTGGACATTTATTTCGAGCGCATGGAGAATTTTGTGCATCGCATC
CATGGGAGGTGATAGTGGCATTGATAACTTTTACTGCCTGTATGTTTAGTGTTGACAAAG
GAAGCAGTTCTGCAAATGATCCGCTAATTAATCCCACAATAAAACCTATTCAAATGAGAC
AGTGTCATGGATGGCGAGAGTCTTGTGATGGCTTCGAAGCTCAATATATTGCAGCAGACG
TAATTTTGATGACAATTGTAAGATGTTCAGCAGTTCTTTATTGCTATTATCAATTCTACA
ATCTCCATAAATTGGGATCAAAATATATTCTTGGTATTGCTGGTCTTTTTACCGTTTTTT
CAAGCTTCATATTTACATCAAGCATTATGAACTTTTTGGAAAGTGACATATCAGATTTAA
AGGATGCATTATTCTTTTTCCTTTTACTCATTGACTTGTCAAAAGCTGGTATTCTTGCAA
AATTGGCATTAAGTGGTTCAAACTCACAAGAAGTTACACAAAACATAGCACGCGGAATGG
AAATTCTCGGACCAGCTATTTCATTGGATACAATGGTTGAAGCTTTGGTGATTGGTGTTG
GAACGCTCTCTGGTGTACAGAGACTAGAAGTTTTAAGTGGATTTGCCGTCATGTCTGTAA
TCGTGAATTATGTTGTGTTCATGACGTTTTATCCAGCTTGTTTATCATTAACACTTGATT
TATCGCGTAATTGCAGCGGAAATAAAGCCGTTGCAGTAAATGCTAATACTGAAACAACAG
AGAAGCAAAAGATTCGTGATCCATCGCTTATTCGAGCCTTAAGTGAAGAAGATCAGAAAC
AAAATCCAATCATACAGCGTGTTAAGCTTATTATGTCAAGCGGTCTTATGATTGTTCATG
CACATAGTCGTCTTACATTTTCTGATAATGATGACGTAGAAGATTCTCATGTCAATGTCA
ACACAAACCCTGGCGCTGACGTAAAGAATCTAAATATGGCTCAACAAATGAACAAAACAG
AGTCGAGTGACATTTCTGACTATATCATGAGATGGTTATCAATTAGTACAG

>g719.t4 Gene=g719 Length=355
MVKTGHLFRAHGEFCASHPWEVIVALITFTACMFSVDKGSSSANDPLINPTIKPIQMRQC
HGWRESCDGFEAQYIAADVILMTIVRCSAVLYCYYQFYNLHKLGSKYILGIAGLFTVFSS
FIFTSSIMNFLESDISDLKDALFFFLLLIDLSKAGILAKLALSGSNSQEVTQNIARGMEI
LGPAISLDTMVEALVIGVGTLSGVQRLEVLSGFAVMSVIVNYVVFMTFYPACLSLTLDLS
RNCSGNKAVAVNANTETTEKQKIRDPSLIRALSEEDQKQNPIIQRVKLIMSSGLMIVHAH
SRLTFSDNDDVEDSHVNVNTNPGADVKNLNMAQQMNKTESSDISDYIMRWLSIST

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g719.t4 PANTHER PTHR46378 STEROL REGULATORY ELEMENT-BINDING PROTEIN CLEAVAGE-ACTIVATING PROTEIN 77 242 5.6E-13
1 g719.t4 Pfam PF12349 Sterol-sensing domain of SREBP cleavage-activation 104 237 1.3E-16
11 g719.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
21 g719.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 36 -
15 g719.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 37 73 -
17 g719.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 95 -
12 g719.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 96 106 -
19 g719.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 107 130 -
16 g719.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 131 141 -
20 g719.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 142 162 -
10 g719.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 163 182 -
18 g719.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 183 204 -
14 g719.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 205 209 -
22 g719.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 210 232 -
13 g719.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 233 355 -
9 g719.t4 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 32 5.0
8 g719.t4 ProSiteProfiles PS50156 Sterol-sensing domain (SSD) profile. 78 235 36.612
4 g719.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 79 98 -
7 g719.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 108 130 -
6 g719.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
3 g719.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 180 202 -
5 g719.t4 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:0032934 sterol binding MF
GO:0005789 endoplasmic reticulum membrane CC
GO:0032933 SREBP signaling pathway BP
GO:0000139 Golgi membrane CC

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.

Raw TPM values