Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2.

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.t5 TTS g10890.t5 12449828 12449828
chr_1 g10890 g10890.t5 isoform g10890.t5 12450009 12453347
chr_1 g10890 g10890.t5 exon g10890.t5.exon1 12450009 12450261
chr_1 g10890 g10890.t5 cds g10890.t5.CDS1 12450009 12450261
chr_1 g10890 g10890.t5 exon g10890.t5.exon2 12452190 12452419
chr_1 g10890 g10890.t5 cds g10890.t5.CDS2 12452190 12452419
chr_1 g10890 g10890.t5 exon g10890.t5.exon3 12452912 12453019
chr_1 g10890 g10890.t5 cds g10890.t5.CDS3 12452912 12453019
chr_1 g10890 g10890.t5 exon g10890.t5.exon4 12453250 12453347
chr_1 g10890 g10890.t5 TSS g10890.t5 12453445 12453445

Sequences

>g10890.t5 Gene=g10890 Length=689
ATGTCATCAGAAGCGGAAAGAAAAAGTCAAAGATCTCGTGAACCATCGCAGTTTGCAAAA
TTCTATTTGATTTTGTATAATGCAGTGCAAGTTGCTGGATGGTCTTTTATGTTGTTTCAA
CTCATCTCTTACTACACAATCGATCGCGATATTCAATCAAAGACATCTCTTTGGGAATAC
ATTGGTTGGACAGTAATCATTTTTCAATTCTTCATGTAGCAATTGGAATTGTTAAAAGCA
ACTTATTCATCACTACAATGCAAGTTTTATCGCGTGTTATGGTTGTTTGTGGTGTTGTGA
TTGCTACCCCTACTGGAAAAGTATCTCCTGGTTTACCTTTAGCTCTGCTAGCATGGAGCG
TCACTGAAATCATTCGATATGGATATTATGCTTTCAATTTACTTGGATCAGTGCCACATA
TTTTAGTATACTTAAGATACACAACATTCATCGCTTTATATCCAATTGGAGTTACCGGAG
AGCTATTATGCTTTTATTGGGCTCAAAGTTATGTCAGAGAAAACAAGTTATGGAGCGTTG
AATTGCCAAATTCAATCAATTTTACATTCTCATACTTTTATTTCATGTGGGGAGTCATGC
TTTCATACATTCCACTCTTTCCTCAAATGTACTTGCACATGTTTGGACAACGTAAAAAGA
TCCTTGGTGGTGGCTCAGGAAGTCACTAA

>g10890.t5 Gene=g10890 Length=196
MVFYVVSTHLLLHNRSRYSIKDISLGIHWLDSNHFSILHVAIGIVKSNLFITTMQVLSRV
MVVCGVVIATPTGKVSPGLPLALLAWSVTEIIRYGYYAFNLLGSVPHILVYLRYTTFIAL
YPIGVTGELLCFYWAQSYVRENKLWSVELPNSINFTFSYFYFMWGVMLSYIPLFPQMYLH
MFGQRKKILGGGSGSH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g10890.t5 PANTHER PTHR11035 PTPLA DOMAIN PROTEIN 35 191 3.5E-54
3 g10890.t5 PANTHER PTHR11035:SF3 VERY-LONG-CHAIN (3R)-3-HYDROXYACYL-COA DEHYDRATASE 35 191 3.5E-54
1 g10890.t5 Pfam PF04387 Protein tyrosine phosphatase-like protein, PTPLA 36 190 1.6E-53
9 g10890.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 55 -
15 g10890.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 56 74 -
12 g10890.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 75 93 -
16 g10890.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 94 112 -
8 g10890.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 113 118 -
13 g10890.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 119 139 -
11 g10890.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 140 158 -
14 g10890.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 159 179 -
10 g10890.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 180 196 -
4 g10890.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 56 75 -
6 g10890.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
5 g10890.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -
7 g10890.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 159 181 -

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. There were no conditions that were differentially expressed