General information for g4006.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Dolichyldiphosphatase 1.
Parent gene
- The parent gene g4006 is located on chr_3: 29485745..29486709 (+ 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_3 | g4006 | g4006.t1 | TSS | g4006.t1 | 29485664 | 29485664 |
| chr_3 | g4006 | g4006.t1 | isoform | g4006.t1 | 29485745 | 29486709 |
| chr_3 | g4006 | g4006.t1 | exon | g4006.t1.exon1 | 29485745 | 29485814 |
| chr_3 | g4006 | g4006.t1 | cds | g4006.t1.CDS1 | 29485745 | 29485814 |
| chr_3 | g4006 | g4006.t1 | exon | g4006.t1.exon2 | 29485907 | 29486007 |
| chr_3 | g4006 | g4006.t1 | cds | g4006.t1.CDS2 | 29485907 | 29486007 |
| chr_3 | g4006 | g4006.t1 | exon | g4006.t1.exon3 | 29486117 | 29486295 |
| chr_3 | g4006 | g4006.t1 | cds | g4006.t1.CDS3 | 29486117 | 29486295 |
| chr_3 | g4006 | g4006.t1 | exon | g4006.t1.exon4 | 29486364 | 29486709 |
| chr_3 | g4006 | g4006.t1 | cds | g4006.t1.CDS4 | 29486364 | 29486709 |
| chr_3 | g4006 | g4006.t1 | TTS | g4006.t1 | 29486901 | 29486901 |
Sequences
>g4006.t1 Gene=g4006 Length=696
ATGAACGAATATGTGTATAATGAATCAGAATGGAAGTCTCTTTCATTGACCTTAGTAGAA
TATCCTAGGAATGATGTTTTTGGTAAATTTATGGCAATTTTAGCGCTCGCTCCATTGTAT
ATTATTGCAACCTTTTCTACAATATCACTTAGATGTCGAGATTTGCATACGATTTTCTAC
TTTATTGGAATTCTACTCAATGAAGCTTTAAACATGACTCTCAAATATTTGATAAAAGAA
CCTCGTCCAGCTGTACGAGACAACTATTACGTTCAATTTGGAATGCCATCATCGCACAGT
CAATTTATGTTATTTTTTACAACATATAGTATACTATTTTTATTTAAAAGATTACATCAG
AATTCGCTAGTGGAAAGAATCTTTAGAGGTATTATTGTTATTTTGATGATAATTGTAACA
GCACTTATCTGTTATGGACGACTTTATTTAATGTATCATACATTAAGTCAAGTTATAGTT
GGTGCAATTATTGGTTTTATGACTGCCCTTATTTGGTTTGTTTTTGTACACTCAATATTG
ACCCCATACGTCTTCCCGAAAATTGTTTCGTGGAGAATCTCAGAAATTTTACTCATTCGT
GATACCTCTCTTATTCCGAATATAGTCTTTTTCGAATACACGGCAACTCGTCAAGAAAGT
CGAGCAAGACTAAGAAAAAATATGAAAATGCAATAG
>g4006.t1 Gene=g4006 Length=231
MNEYVYNESEWKSLSLTLVEYPRNDVFGKFMAILALAPLYIIATFSTISLRCRDLHTIFY
FIGILLNEALNMTLKYLIKEPRPAVRDNYYVQFGMPSSHSQFMLFFTTYSILFLFKRLHQ
NSLVERIFRGIIVILMIIVTALICYGRLYLMYHTLSQVIVGAIIGFMTALIWFVFVHSIL
TPYVFPKIVSWRISEILLIRDTSLIPNIVFFEYTATRQESRARLRKNMKMQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g4006.t1 | CDD | cd03382 | PAP2_dolichyldiphosphatase | 14 | 173 | 3.43172E-49 |
| 5 | g4006.t1 | Gene3D | G3DSA:1.20.144.10 | - | 86 | 192 | 7.0E-18 |
| 2 | g4006.t1 | PANTHER | PTHR11247:SF1 | DOLICHYLDIPHOSPHATASE 1 | 9 | 222 | 1.8E-55 |
| 3 | g4006.t1 | PANTHER | PTHR11247 | PALMITOYL-PROTEIN THIOESTERASE/DOLICHYLDIPHOSPHATASE 1 | 9 | 222 | 1.8E-55 |
| 1 | g4006.t1 | Pfam | PF01569 | PAP2 superfamily | 60 | 176 | 6.1E-16 |
| 11 | g4006.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 25 | - |
| 16 | g4006.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 46 | - |
| 6 | g4006.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 47 | 57 | - |
| 14 | g4006.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 58 | 78 | - |
| 10 | g4006.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 79 | 97 | - |
| 15 | g4006.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 98 | 115 | - |
| 8 | g4006.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 116 | 126 | - |
| 13 | g4006.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 127 | 152 | - |
| 9 | g4006.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 153 | 157 | - |
| 12 | g4006.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 185 | - |
| 7 | g4006.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 186 | 231 | - |
| 23 | g4006.t1 | SMART | SM00014 | acid_phosph_2 | 57 | 173 | 4.2E-14 |
| 4 | g4006.t1 | SUPERFAMILY | SSF48317 | Acid phosphatase/Vanadium-dependent haloperoxidase | 20 | 176 | 1.96E-18 |
| 18 | g4006.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 30 | 49 | - |
| 21 | g4006.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 56 | 78 | - |
| 19 | g4006.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 115 | - |
| 20 | g4006.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 127 | 149 | - |
| 22 | g4006.t1 | 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
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016787 | hydrolase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K07252 (dolichyldiphosphatase)
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.
