Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein Mpv17.

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 g11645 g11645.t1 TTS g11645.t1 17610036 17610036
chr_1 g11645 g11645.t1 isoform g11645.t1 17610166 17610926
chr_1 g11645 g11645.t1 exon g11645.t1.exon1 17610166 17610458
chr_1 g11645 g11645.t1 cds g11645.t1.CDS1 17610166 17610458
chr_1 g11645 g11645.t1 exon g11645.t1.exon2 17610523 17610644
chr_1 g11645 g11645.t1 cds g11645.t1.CDS2 17610523 17610644
chr_1 g11645 g11645.t1 exon g11645.t1.exon3 17610702 17610786
chr_1 g11645 g11645.t1 cds g11645.t1.CDS3 17610702 17610786
chr_1 g11645 g11645.t1 exon g11645.t1.exon4 17610863 17610926
chr_1 g11645 g11645.t1 cds g11645.t1.CDS4 17610863 17610926
chr_1 g11645 g11645.t1 TSS g11645.t1 17611018 17611018

Sequences

>g11645.t1 Gene=g11645 Length=564
ATGCTAAGTCAAATTGCAAGAATCTATCAAAATGGTGTTTCAAAATATCCATACTTAGCT
CAAGGCATACAGACAGCAGTATTGATGAGTACGGGTGATATTATTGCCCAAAAGGTCGTC
GAAAAGAAAGCATCCATTGACTATAAACGGAATGGAAATTTTTTATTGATCGGATTTGTT
GGTGGACTTGGTTTGAGAAAATGGTATGGATTTTTGAGCAATTCTATAAAGGGAAATAAT
AAGGCAATAATAGCTGTTAAAAAAGTTGGTGTTGATCAATTGGTTTTTGCACCTATCTTC
ATTGGAGTATTTATCTCAGCAGTTGGCATGCTACAAGGAAGCAAACCCAATGAAATAAAG
AAAAAATTAGAAAGAGAATATCCTGATATATTAAAAGCTAATTATAAAATATGGCCAGCA
GTACAGCTCATAAACTTTGCTTTTGTTCCTTTAAATTATCAAGTTGTACTTGTTCAAGTA
ATTGCGATTCTATGGAACACATATATAAGTTTTAAAACTAACGAAAATACATCACCAAAT
GGTGATTATAATGCAAGATTATAA

>g11645.t1 Gene=g11645 Length=187
MLSQIARIYQNGVSKYPYLAQGIQTAVLMSTGDIIAQKVVEKKASIDYKRNGNFLLIGFV
GGLGLRKWYGFLSNSIKGNNKAIIAVKKVGVDQLVFAPIFIGVFISAVGMLQGSKPNEIK
KKLEREYPDILKANYKIWPAVQLINFAFVPLNYQVVLVQVIAILWNTYISFKTNENTSPN
GDYNARL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g11645.t1 PANTHER PTHR11266 PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 6 177 4.6E-42
1 g11645.t1 Pfam PF04117 Mpv17 / PMP22 family 109 170 1.1E-23
7 g11645.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 51 -
10 g11645.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 69 -
8 g11645.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 70 88 -
9 g11645.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -
6 g11645.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 112 187 -
4 g11645.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 69 -
3 g11645.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -
5 g11645.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -

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

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.

Raw TPM values