General information for g13238.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13238 is located on chr_1: 28733273..28734358 (+ 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 | g13238 | g13238.t1 | isoform | g13238.t1 | 28733273 | 28734201 |
| chr_1 | g13238 | g13238.t1 | exon | g13238.t1.exon1 | 28733273 | 28733533 |
| chr_1 | g13238 | g13238.t1 | cds | g13238.t1.CDS1 | 28733273 | 28733533 |
| chr_1 | g13238 | g13238.t1 | exon | g13238.t1.exon2 | 28733592 | 28733647 |
| chr_1 | g13238 | g13238.t1 | cds | g13238.t1.CDS2 | 28733592 | 28733647 |
| chr_1 | g13238 | g13238.t1 | exon | g13238.t1.exon3 | 28733722 | 28733909 |
| chr_1 | g13238 | g13238.t1 | cds | g13238.t1.CDS3 | 28733722 | 28733909 |
| chr_1 | g13238 | g13238.t1 | exon | g13238.t1.exon4 | 28734062 | 28734201 |
| chr_1 | g13238 | g13238.t1 | cds | g13238.t1.CDS4 | 28734062 | 28734201 |
| chr_1 | g13238 | g13238.t1 | TSS | g13238.t1 | NA | NA |
| chr_1 | g13238 | g13238.t1 | TTS | g13238.t1 | NA | NA |
Sequences
>g13238.t1 Gene=g13238 Length=645
ATGTTCGGAAGAAATAATAGTGAACCACTATGGAAAATTTTTAGAAAGCACCCTATAACA
AGAGGAATGGCATCCTATCTAGTCATATGGCCAACTGCAAATATTATACAACAGACATTA
TGTGAGAAGGATTTTGATTGGTGGAAGGTAGTACGATTTGGATTATATGGATGTTTTATC
ACAGCACCAAGTCTATATTGTTGGGTTAAACTTGCTACATTCATGTATCCAAATAATCAA
CTTCGTCTATGCATGGCTAAAGCACTAATCGAACAAATATCATACACACCACTTGCTATG
TGCACGTTTTTTTATAGTATGACATGGTTAGAAACTTTTTCAGCAGCTGAAGCTTTTCAA
GAAGTAAAAGTGAAATTTCCACCAACTTATTTTACTGCTATTACAATTTGGCCTCTAATT
GGCACCATAAACTTTGCATTCGTACCTGAAAGAAATCGCGTACTTTTTACCTCATGCTTT
TCATTGTTGTGGACGATATATTTAGGAATAATCCAAGGTGCAATGGTAGATGATGATAGT
CCCTATATAAATGCTGGCAGCATAACTATCCTACAGAAAATCATTTTCATAAAAATCGCT
TTATCACGAATAATAGCTAATATAGATTGCAACAATATAGATTAA
>g13238.t1 Gene=g13238 Length=214
MFGRNNSEPLWKIFRKHPITRGMASYLVIWPTANIIQQTLCEKDFDWWKVVRFGLYGCFI
TAPSLYCWVKLATFMYPNNQLRLCMAKALIEQISYTPLAMCTFFYSMTWLETFSAAEAFQ
EVKVKFPPTYFTAITIWPLIGTINFAFVPERNRVLFTSCFSLLWTIYLGIIQGAMVDDDS
PYINAGSITILQKIIFIKIALSRIIANIDCNNID
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g13238.t1 | PANTHER | PTHR11266 | PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 | 12 | 174 | 5.2E-62 |
| 3 | g13238.t1 | PANTHER | PTHR11266:SF75 | IP10007P | 12 | 174 | 5.2E-62 |
| 1 | g13238.t1 | Pfam | PF04117 | Mpv17 / PMP22 family | 110 | 168 | 8.1E-17 |
| 12 | g13238.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 52 | - |
| 15 | g13238.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 76 | - |
| 10 | g13238.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 77 | 87 | - |
| 18 | g13238.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 88 | 110 | - |
| 11 | g13238.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 111 | 129 | - |
| 14 | g13238.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 130 | 147 | - |
| 9 | g13238.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 148 | 153 | - |
| 17 | g13238.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 154 | 176 | - |
| 13 | g13238.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 177 | 181 | - |
| 16 | g13238.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 182 | 201 | - |
| 8 | g13238.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 202 | 214 | - |
| 6 | g13238.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 72 | - |
| 5 | g13238.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 115 | - |
| 4 | g13238.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 130 | 147 | - |
| 7 | g13238.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 154 | 176 | - |
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.
