General information for g13237.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13237 is located on chr_1: 28731877..28732519 (+ 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 | g13237 | g13237.t1 | TSS | g13237.t1 | 28730364 | 28730364 |
| chr_1 | g13237 | g13237.t1 | isoform | g13237.t1 | 28730540 | 28732519 |
| chr_1 | g13237 | g13237.t1 | exon | g13237.t1.exon1 | 28730540 | 28730558 |
| chr_1 | g13237 | g13237.t1 | cds | g13237.t1.CDS1 | 28730540 | 28730558 |
| chr_1 | g13237 | g13237.t1 | exon | g13237.t1.exon2 | 28730621 | 28730837 |
| chr_1 | g13237 | g13237.t1 | cds | g13237.t1.CDS2 | 28730621 | 28730837 |
| chr_1 | g13237 | g13237.t1 | exon | g13237.t1.exon3 | 28730892 | 28731036 |
| chr_1 | g13237 | g13237.t1 | cds | g13237.t1.CDS3 | 28730892 | 28731036 |
| chr_1 | g13237 | g13237.t1 | exon | g13237.t1.exon4 | 28731097 | 28731244 |
| chr_1 | g13237 | g13237.t1 | cds | g13237.t1.CDS4 | 28731097 | 28731244 |
| chr_1 | g13237 | g13237.t1 | exon | g13237.t1.exon5 | 28731496 | 28731563 |
| chr_1 | g13237 | g13237.t1 | cds | g13237.t1.CDS5 | 28731496 | 28731563 |
| chr_1 | g13237 | g13237.t1 | exon | g13237.t1.exon6 | 28731852 | 28732040 |
| chr_1 | g13237 | g13237.t1 | cds | g13237.t1.CDS6 | 28731852 | 28732040 |
| chr_1 | g13237 | g13237.t1 | exon | g13237.t1.exon7 | 28732100 | 28732519 |
| chr_1 | g13237 | g13237.t1 | cds | g13237.t1.CDS7 | 28732100 | 28732519 |
| chr_1 | g13237 | g13237.t1 | TTS | g13237.t1 | 28732729 | 28732729 |
Sequences
>g13237.t1 Gene=g13237 Length=1206
ATGGCAAAAGTTGAAAGAGTTTCACCAATGAACAGCAGTATTGAATCAGTGATTGCATCA
CCAACTTTTCTTAATTCATCAAGTTCATTCAAATTTTTAACTCCTGGAATTGCAAATTTT
CGAAGAAGCTGTTCTCCTTTGAATCTCAACTACTCAAAATCACCAAATCTTAGTCCTATA
AAACCCAAAACACCTCGCTCAGCTTCACCATTTGAATTAAAGAAACGAGATTTAACTAAT
TATCATAAAAGTTTAATTAAGAAGCAAAAGCATGGTTTCATGAATAATGCACAAAACATC
AACGAAATAACACTCAGTGTTAAAGTCATTCTAGAAGAATTAAAATTAACAGAATATATG
CATTTATTTGAGGAAGAAGAGATTTTTCTTGATGTCTTTTTTACTATTTCTGATGATGAC
CTAAAAGCAATTGGGATTGAAAATAAGGAACATCGTAAAAAATTGATTGATTTTATTAAT
TTTAACACACCAAAGAAAAATATTGCTGTCAAGAAGAATACCATGTATCATAGTACTACA
CAACAGTGTTTTGAAGTGTTGACAACTACAGACAATTTGACTAAAACTTGTAAAAAGATG
ATTTCTAGAGTATCCTCTTTTTTTCGTGCTCATCCAATGTTGAAAGGTATGGCCGTTTAT
GCATTTATCTGGCCAACAAGTGCAAGCATACAGCAATTGATCAATAAAGAAGAATTTGAT
TGGAAGAAATGCTTTAGATTCTTTCTTTTTGGAACATTTTTTGTAGCTCCATCACTTTAC
GGATGGGTTCATCTGTCATCGAACATGTGGAGTGAAATGACTTTAAAAACAGGGATTACA
AAAGCTGTTGTTGAACAATTTTCTTATGGACCAGCTGCAAGTGTGAGTTTTTTTACAATC
ATGACTTTGCTTGAAGGACGATCATTCTCAGAAGCTAAAATGGAAGTTAGAGAGAAATTT
CCTCAAACTTTTCAAGTGGGAGTTTGTTTTTGGCCATTTTTCCAAATTATCAATTTTACG
TTTATTAAAGAACGAAATCGTGTACCTTTCGTAGCATTTGGTAGCTTTATATGGACAATA
TTTCTTGCTTACATGAAAACACTTGATACACAAAAATTACATGAAGTTCATGTTCAAGAA
CATGAACATCCTACACATACGTTCTTTGAAAAGCTTAAAATAAACTTGCAAATCGGTACA
GAATAA
>g13237.t1 Gene=g13237 Length=401
MAKVERVSPMNSSIESVIASPTFLNSSSSFKFLTPGIANFRRSCSPLNLNYSKSPNLSPI
KPKTPRSASPFELKKRDLTNYHKSLIKKQKHGFMNNAQNINEITLSVKVILEELKLTEYM
HLFEEEEIFLDVFFTISDDDLKAIGIENKEHRKKLIDFINFNTPKKNIAVKKNTMYHSTT
QQCFEVLTTTDNLTKTCKKMISRVSSFFRAHPMLKGMAVYAFIWPTSASIQQLINKEEFD
WKKCFRFFLFGTFFVAPSLYGWVHLSSNMWSEMTLKTGITKAVVEQFSYGPAASVSFFTI
MTLLEGRSFSEAKMEVREKFPQTFQVGVCFWPFFQIINFTFIKERNRVPFVAFGSFIWTI
FLAYMKTLDTQKLHEVHVQEHEHPTHTFFEKLKINLQIGTE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g13237.t1 | CDD | cd09487 | SAM_superfamily | 106 | 160 | 1.06067E-10 |
| 6 | g13237.t1 | Gene3D | G3DSA:1.10.150.50 | Transcription Factor | 104 | 160 | 9.8E-13 |
| 3 | g13237.t1 | PANTHER | PTHR11266 | PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 | 199 | 372 | 3.1E-68 |
| 4 | g13237.t1 | PANTHER | PTHR11266:SF75 | IP10007P | 199 | 372 | 3.1E-68 |
| 2 | g13237.t1 | Pfam | PF00536 | SAM domain (Sterile alpha motif) | 111 | 159 | 9.0E-10 |
| 1 | g13237.t1 | Pfam | PF04117 | Mpv17 / PMP22 family | 303 | 362 | 4.5E-18 |
| 9 | g13237.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 243 | - |
| 15 | g13237.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 244 | 263 | - |
| 11 | g13237.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 264 | 282 | - |
| 14 | g13237.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 304 | - |
| 8 | g13237.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 305 | 323 | - |
| 12 | g13237.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 324 | 342 | - |
| 10 | g13237.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 343 | 347 | - |
| 13 | g13237.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 348 | 365 | - |
| 7 | g13237.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 366 | 401 | - |
| 22 | g13237.t1 | ProSiteProfiles | PS50105 | SAM domain profile. | 106 | 160 | 9.741 |
| 5 | g13237.t1 | SUPERFAMILY | SSF47769 | SAM/Pointed domain | 105 | 161 | 7.75E-11 |
| 21 | g13237.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 224 | - |
| 17 | g13237.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 244 | 266 | - |
| 18 | g13237.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 287 | 309 | - |
| 20 | g13237.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 324 | 341 | - |
| 19 | g13237.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 348 | 365 | - |
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:0005515 | protein binding | MF |
| 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.
