General information for g11645.t50
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein Mpv17.
Parent gene
- The parent gene g11645 is located on chr_1: 17610166..17611018 (- 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 | g11645 | g11645.t50 | TTS | g11645.t50 | 17610036 | 17610036 |
| chr_1 | g11645 | g11645.t50 | isoform | g11645.t50 | 17610166 | 17610926 |
| chr_1 | g11645 | g11645.t50 | exon | g11645.t50.exon1 | 17610166 | 17610458 |
| chr_1 | g11645 | g11645.t50 | cds | g11645.t50.CDS1 | 17610166 | 17610458 |
| chr_1 | g11645 | g11645.t50 | exon | g11645.t50.exon2 | 17610523 | 17610644 |
| chr_1 | g11645 | g11645.t50 | cds | g11645.t50.CDS2 | 17610523 | 17610644 |
| chr_1 | g11645 | g11645.t50 | exon | g11645.t50.exon3 | 17610702 | 17610771 |
| chr_1 | g11645 | g11645.t50 | cds | g11645.t50.CDS3 | 17610702 | 17610766 |
| chr_1 | g11645 | g11645.t50 | exon | g11645.t50.exon4 | 17610850 | 17610926 |
| chr_1 | g11645 | g11645.t50 | TSS | g11645.t50 | 17611018 | 17611018 |
Sequences
>g11645.t50 Gene=g11645 Length=562
ATGCTAAGTCAAATTGCAAGAATCTATCAAAATGGTGTTTCAAAATATCCATACTTAGCT
CAAGGTAAATTTTTAAATATTGATGAGTACGGGTGATATTATTGCCCAAAAGGTCGTCGA
AAAGAAAGCATCCATTGACTATAAACGGAATGGAAATTTTTTATTGATCGGATTTGTTGG
TGGACTTGGTTTGAGAAAATGGTATGGATTTTTGAGCAATTCTATAAAGGGAAATAATAA
GGCAATAATAGCTGTTAAAAAAGTTGGTGTTGATCAATTGGTTTTTGCACCTATCTTCAT
TGGAGTATTTATCTCAGCAGTTGGCATGCTACAAGGAAGCAAACCCAATGAAATAAAGAA
AAAATTAGAAAGAGAATATCCTGATATATTAAAAGCTAATTATAAAATATGGCCAGCAGT
ACAGCTCATAAACTTTGCTTTTGTTCCTTTAAATTATCAAGTTGTACTTGTTCAAGTAAT
TGCGATTCTATGGAACACATATATAAGTTTTAAAACTAACGAAAATACATCACCAAATGG
TGATTATAATGCAAGATTATAA
>g11645.t50 Gene=g11645 Length=159
MSTGDIIAQKVVEKKASIDYKRNGNFLLIGFVGGLGLRKWYGFLSNSIKGNNKAIIAVKK
VGVDQLVFAPIFIGVFISAVGMLQGSKPNEIKKKLEREYPDILKANYKIWPAVQLINFAF
VPLNYQVVLVQVIAILWNTYISFKTNENTSPNGDYNARL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g11645.t50 | PANTHER | PTHR11266 | PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 | 1 | 149 | 6.4E-37 |
| 1 | g11645.t50 | Pfam | PF04117 | Mpv17 / PMP22 family | 81 | 142 | 8.1E-24 |
| 7 | g11645.t50 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 23 | - |
| 9 | g11645.t50 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 24 | 41 | - |
| 8 | g11645.t50 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 42 | 60 | - |
| 10 | g11645.t50 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 61 | 83 | - |
| 6 | g11645.t50 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 84 | 159 | - |
| 4 | g11645.t50 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 24 | 41 | - |
| 5 | g11645.t50 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 61 | 83 | - |
| 3 | g11645.t50 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 137 | - |
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:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K13348 (protein Mpv17)
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. There were no conditions that were differentially expressed