General information for g9674.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase.
Parent gene
- The parent gene g9674 is located on chr_1: 4535802..4536998 (+ 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 | g9674 | g9674.t1 | TSS | g9674.t1 | 4535584 | 4535584 |
| chr_1 | g9674 | g9674.t1 | isoform | g9674.t1 | 4535665 | 4536888 |
| chr_1 | g9674 | g9674.t1 | exon | g9674.t1.exon1 | 4535665 | 4535742 |
| chr_1 | g9674 | g9674.t1 | cds | g9674.t1.CDS1 | 4535665 | 4535742 |
| chr_1 | g9674 | g9674.t1 | exon | g9674.t1.exon2 | 4535802 | 4535996 |
| chr_1 | g9674 | g9674.t1 | cds | g9674.t1.CDS2 | 4535802 | 4535996 |
| chr_1 | g9674 | g9674.t1 | exon | g9674.t1.exon3 | 4536055 | 4536888 |
| chr_1 | g9674 | g9674.t1 | cds | g9674.t1.CDS3 | 4536055 | 4536888 |
| chr_1 | g9674 | g9674.t1 | TTS | g9674.t1 | 4537002 | 4537002 |
Sequences
>g9674.t1 Gene=g9674 Length=1107
ATGTCAATCAGTCCATTTGTTTATTGGGCTCAAACAGAAGATCAGATTTCTTTAAAAATT
GATCTTAAAGATGTCAAAGATTTCAACATAAAGAGTGACGAAGCAAAATTCAATTTCACA
GGAGTTGGAGTTGGCGCGAGAGGTTTGCAAGAATATAAATTTTCACTAGACTTGTTCAGT
GAAGTCAAATTTGAAGGAATAAAATCAATTAAGACTGACAACAAAGTTGATGTTTTCATA
CCAAAAAAGGAAAAAGGATTTTGGAATCGATTGATTTGTCAACAGCAAAAGCCATCATGG
TTGAAAATTGATTTTGATAGATGGAAGTCAGAAGATATGGACGACGATGATGATGATGAG
AAACCAAGGAATATAATGCAGGATTATCCAGACATGTTTGATCGATTGCAAAAAGAAGAA
CTTGGATTTCGTAGAGAAAATTTCAAGAAAGTTTACTTAATTCTCTACAATTTATTCCAA
TTTGTTGGTTTTACATATATTTTAGTCGTTATGGGAATTCGTTATTCACGTGATGGTGTT
CATTCAATTCCTGGAACTTATGAGGCAGTAGGAAATGCTTTTAAATTTATTCAATTATTG
CAATATTTAGAAGTGATGCATCCAATTTTTGGTTACACAAAGGGTGGTGCTTTAGTTCCT
TTCTTACAAGTCACAGGACGAAATTTCATTCTTTTTATTATGCTCGATTATGAGCCAAGA
ATGTTGACAAAGCCTGTCGTATTTTATTTATTCCTTGTATGGGCATCAATTGAGATTGTT
CGCTATCCATATTATCTTACACAATTGTTCAAATTTGAAATTGGTTTGCTCACTTGGTTA
CGCTATTCATTATGGATTCCTCTTTATCCGCTTGGTGTTTTATGTGAAGGAATTATTATT
TTGAGAAATATTCCATATTTTGAAGAGACTAAAAGATTGTCAATGACACTGCCTAACAAA
TGGAACTTTACTTTTGATATGCCGACTTTTCTTTATCTTTACATCAGTTTCCTAATTCTT
CCTGGTATAATTTTCATAATGTCTCATATGCAAAAAGTTCGAACCAAAAAACTTGGTGGA
CGAAAGAAAAGCGCTAAATATGATTAA
>g9674.t1 Gene=g9674 Length=368
MSISPFVYWAQTEDQISLKIDLKDVKDFNIKSDEAKFNFTGVGVGARGLQEYKFSLDLFS
EVKFEGIKSIKTDNKVDVFIPKKEKGFWNRLICQQQKPSWLKIDFDRWKSEDMDDDDDDE
KPRNIMQDYPDMFDRLQKEELGFRRENFKKVYLILYNLFQFVGFTYILVVMGIRYSRDGV
HSIPGTYEAVGNAFKFIQLLQYLEVMHPIFGYTKGGALVPFLQVTGRNFILFIMLDYEPR
MLTKPVVFYLFLVWASIEIVRYPYYLTQLFKFEIGLLTWLRYSLWIPLYPLGVLCEGIII
LRNIPYFEETKRLSMTLPNKWNFTFDMPTFLYLYISFLILPGIIFIMSHMQKVRTKKLGG
RKKSAKYD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g9674.t1 | CDD | cd06465 | p23_hB-ind1_like | 5 | 111 | 8.51901E-29 |
| 5 | g9674.t1 | Gene3D | G3DSA:2.60.40.790 | - | 3 | 125 | 1.5E-28 |
| 2 | g9674.t1 | PANTHER | PTHR11035 | PTPLA DOMAIN PROTEIN | 148 | 364 | 4.0E-65 |
| 3 | g9674.t1 | PANTHER | PTHR11035:SF35 | VERY-LONG-CHAIN (3R)-3-HYDROXYACYL-COA DEHYDRATASE | 148 | 364 | 4.0E-65 |
| 1 | g9674.t1 | Pfam | PF04387 | Protein tyrosine phosphatase-like protein, PTPLA | 198 | 359 | 8.4E-44 |
| 8 | g9674.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 150 | - |
| 12 | g9674.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 151 | 173 | - |
| 9 | g9674.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 174 | 245 | - |
| 14 | g9674.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 246 | 264 | - |
| 6 | g9674.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 265 | 283 | - |
| 11 | g9674.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 284 | 307 | - |
| 10 | g9674.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 308 | 326 | - |
| 13 | g9674.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 327 | 347 | - |
| 7 | g9674.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 348 | 368 | - |
| 20 | g9674.t1 | ProSiteProfiles | PS51203 | CS domain profile. | 2 | 92 | 14.104 |
| 4 | g9674.t1 | SUPERFAMILY | SSF49764 | HSP20-like chaperones | 1 | 132 | 1.92E-25 |
| 18 | g9674.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 151 | 173 | - |
| 17 | g9674.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 246 | 265 | - |
| 19 | g9674.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 285 | 307 | - |
| 16 | g9674.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 328 | 350 | - |
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.
