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.t7 TSS g9674.t7 4535584 4535584
chr_1 g9674 g9674.t7 isoform g9674.t7 4535802 4536998
chr_1 g9674 g9674.t7 exon g9674.t7.exon1 4535802 4536998
chr_1 g9674 g9674.t7 cds g9674.t7.CDS1 4536118 4536888
chr_1 g9674 g9674.t7 TTS g9674.t7 4537002 4537002

Sequences

>g9674.t7 Gene=g9674 Length=1197
GATTTCAACATAAAGAGTGACGAAGCAAAATTCAATTTCACAGGAGTTGGAGTTGGCGCG
AGAGGTTTGCAAGAATATAAATTTTCACTAGACTTGTTCAGTGAAGTCAAATTTGAAGGA
ATAAAATCAATTAAGACTGACAACAAAGTTGATGTTTTCATACCAAAAAAGGAAAAAGGA
TTTTGGAATCGATTGGTAAAATTGAGAAAGAAACAAAAAATTTAAATTTTTAATTCAAAA
AAATTGTTTTTAGATTTGTCAACAGCAAAAGCCATCATGGTTGAAAATTGATTTTGATAG
ATGGAAGTCAGAAGATATGGACGACGATGATGATGATGAGAAACCAAGGAATATAATGCA
GGATTATCCAGACATGTTTGATCGATTGCAAAAAGAAGAACTTGGATTTCGTAGAGAAAA
TTTCAAGAAAGTTTACTTAATTCTCTACAATTTATTCCAATTTGTTGGTTTTACATATAT
TTTAGTCGTTATGGGAATTCGTTATTCACGTGATGGTGTTCATTCAATTCCTGGAACTTA
TGAGGCAGTAGGAAATGCTTTTAAATTTATTCAATTATTGCAATATTTAGAAGTGATGCA
TCCAATTTTTGGTTACACAAAGGGTGGTGCTTTAGTTCCTTTCTTACAAGTCACAGGACG
AAATTTCATTCTTTTTATTATGCTCGATTATGAGCCAAGAATGTTGACAAAGCCTGTCGT
ATTTTATTTATTCCTTGTATGGGCATCAATTGAGATTGTTCGCTATCCATATTATCTTAC
ACAATTGTTCAAATTTGAAATTGGTTTGCTCACTTGGTTACGCTATTCATTATGGATTCC
TCTTTATCCGCTTGGTGTTTTATGTGAAGGAATTATTATTTTGAGAAATATTCCATATTT
TGAAGAGACTAAAAGATTGTCAATGACACTGCCTAACAAATGGAACTTTACTTTTGATAT
GCCGACTTTTCTTTATCTTTACATCAGTTTCCTAATTCTTCCTGGTATAATTTTCATAAT
GTCTCATATGCAAAAAGTTCGAACCAAAAAACTTGGTGGACGAAAGAAAAGCGCTAAATA
TGATTAAAAATCTTGATTAAAATATTCTTGAATGAATAAGGATTTTTTTAAAAGCAAACT
TTCAAAATCTGTTTTTGTAACTTGGCTTGTCAATCGATTTTAATAAAATAAAGAAAA

>g9674.t7 Gene=g9674 Length=256
MDDDDDDEKPRNIMQDYPDMFDRLQKEELGFRRENFKKVYLILYNLFQFVGFTYILVVMG
IRYSRDGVHSIPGTYEAVGNAFKFIQLLQYLEVMHPIFGYTKGGALVPFLQVTGRNFILF
IMLDYEPRMLTKPVVFYLFLVWASIEIVRYPYYLTQLFKFEIGLLTWLRYSLWIPLYPLG
VLCEGIIILRNIPYFEETKRLSMTLPNKWNFTFDMPTFLYLYISFLILPGIIFIMSHMQK
VRTKKLGGRKKSAKYD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g9674.t7 PANTHER PTHR11035 PTPLA DOMAIN PROTEIN 36 252 4.8E-64
3 g9674.t7 PANTHER PTHR11035:SF35 VERY-LONG-CHAIN (3R)-3-HYDROXYACYL-COA DEHYDRATASE 36 252 4.8E-64
1 g9674.t7 Pfam PF04387 Protein tyrosine phosphatase-like protein, PTPLA 86 247 3.2E-44
10 g9674.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 38 -
13 g9674.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 39 61 -
11 g9674.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 62 133 -
16 g9674.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 134 152 -
8 g9674.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 153 171 -
15 g9674.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 195 -
12 g9674.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 196 214 -
14 g9674.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 215 235 -
9 g9674.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 236 256 -
6 g9674.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 61 -
4 g9674.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 134 153 -
5 g9674.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -
7 g9674.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 216 238 -

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