General information for g4006.t10
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.t10 | TSS | g4006.t10 | 29485664 | 29485664 |
| chr_3 | g4006 | g4006.t10 | isoform | g4006.t10 | 29485745 | 29486709 |
| chr_3 | g4006 | g4006.t10 | exon | g4006.t10.exon1 | 29485745 | 29486295 |
| chr_3 | g4006 | g4006.t10 | cds | g4006.t10.CDS1 | 29486159 | 29486295 |
| chr_3 | g4006 | g4006.t10 | exon | g4006.t10.exon2 | 29486364 | 29486709 |
| chr_3 | g4006 | g4006.t10 | cds | g4006.t10.CDS2 | 29486364 | 29486709 |
| chr_3 | g4006 | g4006.t10 | TTS | g4006.t10 | 29486901 | 29486901 |
Sequences
>g4006.t10 Gene=g4006 Length=897
ATGAACGAATATGTGTATAATGAATCAGAATGGAAGTCTCTTTCATTGACCTTAGTAGAA
TATCCTAGGAGTAAGTGTATTTAAATTAATTTATGTTTGCATAATTATACACATTGACAA
CACAAATCTCATTTGACCTAACATTTCAACTTTTATTTATAGATGATGTTTTTGGTAAAT
TTATGGCAATTTTAGCGCTCGCTCCATTGTATATTATTGCAACCTTTTCTACAATATCAC
TTAGATGTCGAGATTTGCATACGGTGAGTAAATAAAATTATTCTGACATCAGCAATTGTG
TGTGCGTGCTTTTTTTGTTGCAAAAAGCAAAGTTCAATGAATGAGTGTCTCTCATTTACA
TATTTATCATAGATTTTCTACTTTATTGGAATTCTACTCAATGAAGCTTTAAACATGACT
CTCAAATATTTGATAAAAGAACCTCGTCCAGCTGTACGAGACAACTATTACGTTCAATTT
GGAATGCCATCATCGCACAGTCAATTTATGTTATTTTTTACAACATATAGTATACTATTT
TTATTTAAAAGATTACATCAGAATTCGCTAGTGGAAAGAATCTTTAGAGGTATTATTGTT
ATTTTGATGATAATTGTAACAGCACTTATCTGTTATGGACGACTTTATTTAATGTATCAT
ACATTAAGTCAAGTTATAGTTGGTGCAATTATTGGTTTTATGACTGCCCTTATTTGGTTT
GTTTTTGTACACTCAATATTGACCCCATACGTCTTCCCGAAAATTGTTTCGTGGAGAATC
TCAGAAATTTTACTCATTCGTGATACCTCTCTTATTCCGAATATAGTCTTTTTCGAATAC
ACGGCAACTCGTCAAGAAAGTCGAGCAAGACTAAGAAAAAATATGAAAATGCAATAG
>g4006.t10 Gene=g4006 Length=160
MTLKYLIKEPRPAVRDNYYVQFGMPSSHSQFMLFFTTYSILFLFKRLHQNSLVERIFRGI
IVILMIIVTALICYGRLYLMYHTLSQVIVGAIIGFMTALIWFVFVHSILTPYVFPKIVSW
RISEILLIRDTSLIPNIVFFEYTATRQESRARLRKNMKMQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4006.t10 | Gene3D | G3DSA:1.20.144.10 | - | 15 | 121 | 3.7E-18 |
| 2 | g4006.t10 | PANTHER | PTHR11247:SF1 | DOLICHYLDIPHOSPHATASE 1 | 3 | 151 | 2.6E-36 |
| 3 | g4006.t10 | PANTHER | PTHR11247 | PALMITOYL-PROTEIN THIOESTERASE/DOLICHYLDIPHOSPHATASE 1 | 3 | 151 | 2.6E-36 |
| 1 | g4006.t10 | Pfam | PF01569 | PAP2 superfamily | 3 | 106 | 1.9E-14 |
| 12 | g4006.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 26 | - |
| 15 | g4006.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 44 | - |
| 11 | g4006.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 45 | 55 | - |
| 16 | g4006.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 56 | 81 | - |
| 13 | g4006.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 82 | 86 | - |
| 14 | g4006.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 114 | - |
| 10 | g4006.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 115 | 160 | - |
| 8 | g4006.t10 | SMART | SM00014 | acid_phosph_2 | 1 | 102 | 1.6E-5 |
| 7 | g4006.t10 | SUPERFAMILY | SSF48317 | Acid phosphatase/Vanadium-dependent haloperoxidase | 2 | 105 | 4.19E-14 |
| 4 | g4006.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 44 | - |
| 5 | g4006.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 56 | 78 | - |
| 6 | g4006.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 88 | 110 | - |
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 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