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.t4 TTS g10890.t4 12449828 12449828
chr_1 g10890 g10890.t4 isoform g10890.t4 12450009 12453020
chr_1 g10890 g10890.t4 exon g10890.t4.exon1 12450009 12450261
chr_1 g10890 g10890.t4 cds g10890.t4.CDS1 12450009 12450261
chr_1 g10890 g10890.t4 exon g10890.t4.exon2 12452190 12452419
chr_1 g10890 g10890.t4 cds g10890.t4.CDS2 12452190 12452419
chr_1 g10890 g10890.t4 exon g10890.t4.exon3 12452893 12453020
chr_1 g10890 g10890.t4 cds g10890.t4.CDS3 12452893 12453009
chr_1 g10890 g10890.t4 TSS g10890.t4 12453445 12453445

Sequences

>g10890.t4 Gene=g10890 Length=611
GATGGTCTTTTATGTTGTTTCAACTCATCTCTTACTACACAATCGATCGCGATATTCAAT
CAAAGACATCTCTTTGGGAATACATTGGTTGGACAGTAATCATTTTTCAGAATGCGGCAG
TTCTTGAGATTCTTCATGTAGCAATTGGAATTGTTAAAAGCAACTTATTCATCACTACAA
TGCAAGTTTTATCGCGTGTTATGGTTGTTTGTGGTGTTGTGATTGCTACCCCTACTGGAA
AAGTATCTCCTGGTTTACCTTTAGCTCTGCTAGCATGGAGCGTCACTGAAATCATTCGAT
ATGGATATTATGCTTTCAATTTACTTGGATCAGTGCCACATATTTTAGTATACTTAAGAT
ACACAACATTCATCGCTTTATATCCAATTGGAGTTACCGGAGAGCTATTATGCTTTTATT
GGGCTCAAAGTTATGTCAGAGAAAACAAGTTATGGAGCGTTGAATTGCCAAATTCAATCA
ATTTTACATTCTCATACTTTTATTTCATGTGGGGAGTCATGCTTTCATACATTCCACTCT
TTCCTCAAATGTACTTGCACATGTTTGGACAACGTAAAAAGATCCTTGGTGGTGGCTCAG
GAAGTCACTAA

>g10890.t4 Gene=g10890 Length=199
MLFQLISYYTIDRDIQSKTSLWEYIGWTVIIFQNAAVLEILHVAIGIVKSNLFITTMQVL
SRVMVVCGVVIATPTGKVSPGLPLALLAWSVTEIIRYGYYAFNLLGSVPHILVYLRYTTF
IALYPIGVTGELLCFYWAQSYVRENKLWSVELPNSINFTFSYFYFMWGVMLSYIPLFPQM
YLHMFGQRKKILGGGSGSH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g10890.t4 PANTHER PTHR11035 PTPLA DOMAIN PROTEIN 6 194 1.1E-60
3 g10890.t4 PANTHER PTHR11035:SF3 VERY-LONG-CHAIN (3R)-3-HYDROXYACYL-COA DEHYDRATASE 6 194 1.1E-60
1 g10890.t4 Pfam PF04387 Protein tyrosine phosphatase-like protein, PTPLA 33 193 1.5E-57
14 g10890.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 23 -
15 g10890.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 24 47 -
10 g10890.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 58 -
17 g10890.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 77 -
13 g10890.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 78 96 -
19 g10890.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 115 -
11 g10890.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 116 121 -
18 g10890.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 142 -
12 g10890.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 161 -
16 g10890.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 162 182 -
9 g10890.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 183 199 -
5 g10890.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 24 46 -
7 g10890.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -
4 g10890.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -
6 g10890.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 120 142 -
8 g10890.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 162 184 -

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

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.

Raw TPM values