Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase hpo-8.

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_1 g10890 g10890.t3 isoform g10890.t3 12449819 12452389
chr_1 g10890 g10890.t3 exon g10890.t3.exon1 12449819 12450261
chr_1 g10890 g10890.t3 TTS g10890.t3 12449828 12449828
chr_1 g10890 g10890.t3 cds g10890.t3.CDS1 12450009 12450261
chr_1 g10890 g10890.t3 exon g10890.t3.exon2 12452190 12452389
chr_1 g10890 g10890.t3 cds g10890.t3.CDS2 12452190 12452368
chr_1 g10890 g10890.t3 TSS g10890.t3 NA NA

Sequences

>g10890.t3 Gene=g10890 Length=643
AGCAACTTATTCATCACTACAATGCAAGTTTTATCGCGTGTTATGGTTGTTTGTGGTGTT
GTGATTGCTACCCCTACTGGAAAAGTATCTCCTGGTTTACCTTTAGCTCTGCTAGCATGG
AGCGTCACTGAAATCATTCGATATGGATATTATGCTTTCAATTTACTTGGATCAGTGCCA
CATATTTTAGTATACTTAAGATACACAACATTCATCGCTTTATATCCAATTGGAGTTACC
GGAGAGCTATTATGCTTTTATTGGGCTCAAAGTTATGTCAGAGAAAACAAGTTATGGAGC
GTTGAATTGCCAAATTCAATCAATTTTACATTCTCATACTTTTATTTCATGTGGGGAGTC
ATGCTTTCATACATTCCACTCTTTCCTCAAATGTACTTGCACATGTTTGGACAACGTAAA
AAGATCCTTGGTGGTGGCTCAGGAAGTCACTAATAGAAATAATAGGATGATTTTACACTA
CAAAGTTATTAGTTTGTAGTAATTTGAGATTTTTCTTATGGTATGTGGTGGTGCTTGTCA
GTTTGTGAAAGAAAAAAGAAAAATTTTGGTTCAGGGTTGTTTTAAAAGTTTGTACTCGAA
ATTCCTTTTGATAAAATAAAAAATCTTAATTTTTGTTATAAAA

>g10890.t3 Gene=g10890 Length=143
MQVLSRVMVVCGVVIATPTGKVSPGLPLALLAWSVTEIIRYGYYAFNLLGSVPHILVYLR
YTTFIALYPIGVTGELLCFYWAQSYVRENKLWSVELPNSINFTFSYFYFMWGVMLSYIPL
FPQMYLHMFGQRKKILGGGSGSH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g10890.t3 PANTHER PTHR11035 PTPLA DOMAIN PROTEIN 1 138 5.1E-47
3 g10890.t3 PANTHER PTHR11035:SF3 VERY-LONG-CHAIN (3R)-3-HYDROXYACYL-COA DEHYDRATASE 1 138 5.1E-47
1 g10890.t3 Pfam PF04387 Protein tyrosine phosphatase-like protein, PTPLA 1 137 8.7E-46
12 g10890.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
13 g10890.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
14 g10890.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
18 g10890.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
11 g10890.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 25 -
17 g10890.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 46 -
8 g10890.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 57 -
16 g10890.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 58 82 -
10 g10890.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 83 101 -
15 g10890.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 102 126 -
9 g10890.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 143 -
5 g10890.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
6 g10890.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 58 -
7 g10890.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 63 85 -
4 g10890.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 100 122 -

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