Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

Parent gene

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.t11 TSS g13237.t11 28731447 28731447
chr_1 g13237 g13237.t11 isoform g13237.t11 28731496 28732519
chr_1 g13237 g13237.t11 exon g13237.t11.exon1 28731496 28731563
chr_1 g13237 g13237.t11 exon g13237.t11.exon2 28731852 28731942
chr_1 g13237 g13237.t11 exon g13237.t11.exon3 28732075 28732519
chr_1 g13237 g13237.t11 cds g13237.t11.CDS1 28732118 28732519
chr_1 g13237 g13237.t11 TTS g13237.t11 28732729 28732729

Sequences

>g13237.t11 Gene=g13237 Length=604
ATAGTACTACACAACAGTGTTTTGAAGTGTTGACAACTACAGACAATTTGACTAAAACTT
GTAAAAAGATGATTTCTAGAGTATCCTCTTTTTTTCGTGCTCATCCAATGTTGAAAGGTA
TGGCCGTTTATGCATTTATCTGGCCAACAAGTGCAAGCAGTGACTAAAATTATTACCGTT
CTAGGTTCATCTGTCATCGAACATGTGGAGTGAAATGACTTTAAAAACAGGGATTACAAA
AGCTGTTGTTGAACAATTTTCTTATGGACCAGCTGCAAGTGTGAGTTTTTTTACAATCAT
GACTTTGCTTGAAGGACGATCATTCTCAGAAGCTAAAATGGAAGTTAGAGAGAAATTTCC
TCAAACTTTTCAAGTGGGAGTTTGTTTTTGGCCATTTTTCCAAATTATCAATTTTACGTT
TATTAAAGAACGAAATCGTGTACCTTTCGTAGCATTTGGTAGCTTTATATGGACAATATT
TCTTGCTTACATGAAAACACTTGATACACAAAAATTACATGAAGTTCATGTTCAAGAACA
TGAACATCCTACACATACGTTCTTTGAAAAGCTTAAAATAAACTTGCAAATCGGTACAGA
ATAA

>g13237.t11 Gene=g13237 Length=133
MWSEMTLKTGITKAVVEQFSYGPAASVSFFTIMTLLEGRSFSEAKMEVREKFPQTFQVGV
CFWPFFQIINFTFIKERNRVPFVAFGSFIWTIFLAYMKTLDTQKLHEVHVQEHEHPTHTF
FEKLKINLQIGTE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13237.t11 PANTHER PTHR11266 PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 1 104 2.2E-40
3 g13237.t11 PANTHER PTHR11266:SF75 IP10007P 1 104 2.2E-40
1 g13237.t11 Pfam PF04117 Mpv17 / PMP22 family 35 94 5.6E-19
10 g13237.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
13 g13237.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 36 -
8 g13237.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 37 55 -
12 g13237.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 56 74 -
9 g13237.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 75 79 -
11 g13237.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 80 97 -
7 g13237.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 98 133 -
5 g13237.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 19 41 -
6 g13237.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 56 73 -
4 g13237.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 80 97 -

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 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.

Raw TPM values