Gene loci information

Transcript annotation

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

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 g9674 g9674.t4 TSS g9674.t4 4535584 4535584
chr_1 g9674 g9674.t4 isoform g9674.t4 4535665 4536888
chr_1 g9674 g9674.t4 exon g9674.t4.exon1 4535665 4535742
chr_1 g9674 g9674.t4 exon g9674.t4.exon2 4535802 4535961
chr_1 g9674 g9674.t4 exon g9674.t4.exon3 4536163 4536888
chr_1 g9674 g9674.t4 cds g9674.t4.CDS1 4536175 4536888
chr_1 g9674 g9674.t4 TTS g9674.t4 4537002 4537002

Sequences

>g9674.t4 Gene=g9674 Length=964
ATGTCAATCAGTCCATTTGTTTATTGGGCTCAAACAGAAGATCAGATTTCTTTAAAAATT
GATCTTAAAGATGTCAAAGATTTCAACATAAAGAGTGACGAAGCAAAATTCAATTTCACA
GGAGTTGGAGTTGGCGCGAGAGGTTTGCAAGAATATAAATTTTCACTAGACTTGTTCAGT
GAAGTCAAATTTGAAGGAATAAAATCAATTAAGACTGACAACAAAGTTGATGTTTTCAGA
TTATCCAGACATGTTTGATCGATTGCAAAAAGAAGAACTTGGATTTCGTAGAGAAAATTT
CAAGAAAGTTTACTTAATTCTCTACAATTTATTCCAATTTGTTGGTTTTACATATATTTT
AGTCGTTATGGGAATTCGTTATTCACGTGATGGTGTTCATTCAATTCCTGGAACTTATGA
GGCAGTAGGAAATGCTTTTAAATTTATTCAATTATTGCAATATTTAGAAGTGATGCATCC
AATTTTTGGTTACACAAAGGGTGGTGCTTTAGTTCCTTTCTTACAAGTCACAGGACGAAA
TTTCATTCTTTTTATTATGCTCGATTATGAGCCAAGAATGTTGACAAAGCCTGTCGTATT
TTATTTATTCCTTGTATGGGCATCAATTGAGATTGTTCGCTATCCATATTATCTTACACA
ATTGTTCAAATTTGAAATTGGTTTGCTCACTTGGTTACGCTATTCATTATGGATTCCTCT
TTATCCGCTTGGTGTTTTATGTGAAGGAATTATTATTTTGAGAAATATTCCATATTTTGA
AGAGACTAAAAGATTGTCAATGACACTGCCTAACAAATGGAACTTTACTTTTGATATGCC
GACTTTTCTTTATCTTTACATCAGTTTCCTAATTCTTCCTGGTATAATTTTCATAATGTC
TCATATGCAAAAAGTTCGAACCAAAAAACTTGGTGGACGAAAGAAAAGCGCTAAATATGA
TTAA

>g9674.t4 Gene=g9674 Length=237
MFDRLQKEELGFRRENFKKVYLILYNLFQFVGFTYILVVMGIRYSRDGVHSIPGTYEAVG
NAFKFIQLLQYLEVMHPIFGYTKGGALVPFLQVTGRNFILFIMLDYEPRMLTKPVVFYLF
LVWASIEIVRYPYYLTQLFKFEIGLLTWLRYSLWIPLYPLGVLCEGIIILRNIPYFEETK
RLSMTLPNKWNFTFDMPTFLYLYISFLILPGIIFIMSHMQKVRTKKLGGRKKSAKYD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g9674.t4 PANTHER PTHR11035 PTPLA DOMAIN PROTEIN 14 232 7.5E-64
1 g9674.t4 Pfam PF04387 Protein tyrosine phosphatase-like protein, PTPLA 67 228 2.6E-44
8 g9674.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
12 g9674.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
10 g9674.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 43 114 -
14 g9674.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 133 -
9 g9674.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 134 152 -
13 g9674.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 153 176 -
11 g9674.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 177 195 -
15 g9674.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 196 216 -
7 g9674.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 217 237 -
3 g9674.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
6 g9674.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 134 -
5 g9674.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 154 176 -
4 g9674.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 196 218 -

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