Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t6 isoform g719.t6 5492733 5501085
chr_3 g719 g719.t6 exon g719.t6.exon1 5492733 5492821
chr_3 g719 g719.t6 cds g719.t6.CDS1 5492733 5492821
chr_3 g719 g719.t6 exon g719.t6.exon2 5497030 5497468
chr_3 g719 g719.t6 cds g719.t6.CDS2 5497030 5497357
chr_3 g719 g719.t6 exon g719.t6.exon3 5500772 5501085
chr_3 g719 g719.t6 TSS g719.t6 5501096 5501096
chr_3 g719 g719.t6 TTS g719.t6 NA NA

Sequences

>g719.t6 Gene=g719 Length=842
TTTTTCTTCTCTTTCATCTAAAATAGATGTTTTAAGACATGTTGCTGCTGATTTTCTCTA
GTACTTATAAAACAGAACATGCCAAATATTGAAATGAAACATCAGCACAAGTGAATTAAA
TAATAGAAAAAGTGACAAAAGTTACATAAAATATAATTGTATAAGAATAGAGAAGAATTC
CTATATGAAAGTGTGAAAGTGAAAAAGAAAAATTCGTGAAAATTCTATCTTATCTCTTGA
ATAAAAAAATTTTGACTTGTGCAAAAAATCTGTTAATAAATAAAGTCAATTAAAATATAA
AGCGACAAGTACAGAGGAAAAAACTTCATTCATCGATTAAAAATTAATCAACAATACTGC
TTAGTGTTACTACTTTAAATTAATTACTTCAACGTCAAAACTTGTTAATAAATCTATAAA
TCAAAATGGTGAAAACTGGACATTTATTTCGAGCGCATGGAGAATTTTGTGCATCGCATC
CATGGGAGGTGATAGTGGCATTGATAACTTTTACTGCCTGTATGTTTAGTGTTGACAAAG
GAAGCAGTTCTGCAAATGATCCGCTAATTAATCCCACAATAAAACCTATTCAAATGAGAC
AGTGTCATGGATGGCGAGAGTCTTGTGATGGCTTCGAAGCTCAATATATTGCAGCAGACG
TAATTTTGATGACAATTGTAAGATGTTCAGCAGTTCTTTATTGCTATTATCAATTCTACA
ATCTCCATAAATTGGGATCAAAATATATTCTTGGTATTGCTGGTCTTTTTACCGTTTTTT
CAAGCTTCATATTTACATCAAGCATTATGAACTTTTTGGAAAGTGACATATCAGATTTAA
AG

>g719.t6 Gene=g719 Length=139
MVKTGHLFRAHGEFCASHPWEVIVALITFTACMFSVDKGSSSANDPLINPTIKPIQMRQC
HGWRESCDGFEAQYIAADVILMTIVRCSAVLYCYYQFYNLHKLGSKYILGIAGLFTVFSS
FIFTSSIMNFLESDISDLK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g719.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
11 g719.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 36 -
7 g719.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 37 73 -
9 g719.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 95 -
6 g719.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 96 106 -
10 g719.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 107 131 -
8 g719.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 132 139 -
4 g719.t6 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 32 5.0
3 g719.t6 ProSiteProfiles PS50156 Sterol-sensing domain (SSD) profile. 78 139 14.337
2 g719.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -
1 g719.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 108 130 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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