General information for g10890.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2.
Parent gene
- The parent gene g10890 is located on chr_1: 12450009..12453347 (- strand)
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.t1 | TTS | g10890.t1 | 12449828 | 12449828 |
| chr_1 | g10890 | g10890.t1 | isoform | g10890.t1 | 12450009 | 12453347 |
| chr_1 | g10890 | g10890.t1 | exon | g10890.t1.exon1 | 12450009 | 12450261 |
| chr_1 | g10890 | g10890.t1 | cds | g10890.t1.CDS1 | 12450009 | 12450261 |
| chr_1 | g10890 | g10890.t1 | exon | g10890.t1.exon2 | 12452190 | 12452419 |
| chr_1 | g10890 | g10890.t1 | cds | g10890.t1.CDS2 | 12452190 | 12452419 |
| chr_1 | g10890 | g10890.t1 | exon | g10890.t1.exon3 | 12452893 | 12453019 |
| chr_1 | g10890 | g10890.t1 | cds | g10890.t1.CDS3 | 12452893 | 12453019 |
| chr_1 | g10890 | g10890.t1 | exon | g10890.t1.exon4 | 12453250 | 12453347 |
| chr_1 | g10890 | g10890.t1 | cds | g10890.t1.CDS4 | 12453250 | 12453347 |
| chr_1 | g10890 | g10890.t1 | TSS | g10890.t1 | 12453445 | 12453445 |
Sequences
>g10890.t1 Gene=g10890 Length=708
ATGTCATCAGAAGCGGAAAGAAAAAGTCAAAGATCTCGTGAACCATCGCAGTTTGCAAAA
TTCTATTTGATTTTGTATAATGCAGTGCAAGTTGCTGGATGGTCTTTTATGTTGTTTCAA
CTCATCTCTTACTACACAATCGATCGCGATATTCAATCAAAGACATCTCTTTGGGAATAC
ATTGGTTGGACAGTAATCATTTTTCAGAATGCGGCAGTTCTTGAGATTCTTCATGTAGCA
ATTGGAATTGTTAAAAGCAACTTATTCATCACTACAATGCAAGTTTTATCGCGTGTTATG
GTTGTTTGTGGTGTTGTGATTGCTACCCCTACTGGAAAAGTATCTCCTGGTTTACCTTTA
GCTCTGCTAGCATGGAGCGTCACTGAAATCATTCGATATGGATATTATGCTTTCAATTTA
CTTGGATCAGTGCCACATATTTTAGTATACTTAAGATACACAACATTCATCGCTTTATAT
CCAATTGGAGTTACCGGAGAGCTATTATGCTTTTATTGGGCTCAAAGTTATGTCAGAGAA
AACAAGTTATGGAGCGTTGAATTGCCAAATTCAATCAATTTTACATTCTCATACTTTTAT
TTCATGTGGGGAGTCATGCTTTCATACATTCCACTCTTTCCTCAAATGTACTTGCACATG
TTTGGACAACGTAAAAAGATCCTTGGTGGTGGCTCAGGAAGTCACTAA
>g10890.t1 Gene=g10890 Length=235
MSSEAERKSQRSREPSQFAKFYLILYNAVQVAGWSFMLFQLISYYTIDRDIQSKTSLWEY
IGWTVIIFQNAAVLEILHVAIGIVKSNLFITTMQVLSRVMVVCGVVIATPTGKVSPGLPL
ALLAWSVTEIIRYGYYAFNLLGSVPHILVYLRYTTFIALYPIGVTGELLCFYWAQSYVRE
NKLWSVELPNSINFTFSYFYFMWGVMLSYIPLFPQMYLHMFGQRKKILGGGSGSH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g10890.t1 | PANTHER | PTHR11035 | PTPLA DOMAIN PROTEIN | 8 | 229 | 7.2E-72 |
| 1 | g10890.t1 | Pfam | PF04387 | Protein tyrosine phosphatase-like protein, PTPLA | 69 | 229 | 2.6E-57 |
| 10 | g10890.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 20 | - |
| 21 | g10890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 45 | - |
| 15 | g10890.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 46 | 59 | - |
| 18 | g10890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 83 | - |
| 11 | g10890.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 84 | 94 | - |
| 17 | g10890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 95 | 113 | - |
| 14 | g10890.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 114 | 132 | - |
| 20 | g10890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 133 | 151 | - |
| 12 | g10890.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 152 | 157 | - |
| 19 | g10890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 178 | - |
| 13 | g10890.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 179 | 197 | - |
| 16 | g10890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 198 | 218 | - |
| 9 | g10890.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 219 | 235 | - |
| 7 | g10890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 8 | g10890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 58 | 80 | - |
| 4 | g10890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 109 | - |
| 6 | g10890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 129 | 151 | - |
| 3 | g10890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 156 | 178 | - |
| 5 | g10890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 198 | 220 | - |
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 transcript has been annotated with K10703 (very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase)
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.
