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.t46 TTS g11645.t46 17610036 17610036
chr_1 g11645 g11645.t46 isoform g11645.t46 17610166 17610926
chr_1 g11645 g11645.t46 exon g11645.t46.exon1 17610166 17610266
chr_1 g11645 g11645.t46 cds g11645.t46.CDS1 17610249 17610266
chr_1 g11645 g11645.t46 exon g11645.t46.exon2 17610310 17610458
chr_1 g11645 g11645.t46 cds g11645.t46.CDS2 17610310 17610458
chr_1 g11645 g11645.t46 exon g11645.t46.exon3 17610523 17610644
chr_1 g11645 g11645.t46 cds g11645.t46.CDS3 17610523 17610644
chr_1 g11645 g11645.t46 exon g11645.t46.exon4 17610702 17610786
chr_1 g11645 g11645.t46 cds g11645.t46.CDS4 17610702 17610786
chr_1 g11645 g11645.t46 exon g11645.t46.exon5 17610863 17610926
chr_1 g11645 g11645.t46 cds g11645.t46.CDS5 17610863 17610926
chr_1 g11645 g11645.t46 TSS g11645.t46 17611018 17611018

Sequences

>g11645.t46 Gene=g11645 Length=521
ATGCTAAGTCAAATTGCAAGAATCTATCAAAATGGTGTTTCAAAATATCCATACTTAGCT
CAAGGCATACAGACAGCAGTATTGATGAGTACGGGTGATATTATTGCCCAAAAGGTCGTC
GAAAAGAAAGCATCCATTGACTATAAACGGAATGGAAATTTTTTATTGATCGGATTTGTT
GGTGGACTTGGTTTGAGAAAATGGTATGGATTTTTGAGCAATTCTATAAAGGGAAATAAT
AAGGCAATAATAGCTGTTAAAAAAGTTGGTGTTGATCAATTGGTTTTTGCACCTATCTTC
ATTGGAGTATTTATCTCAGCAGTTGGCATGCTACAAGGAAGCAAACCCAATGAAATAAAG
AAAAAATTAGAAAGAGAATATCCTGATATATTAAAAGCTAATTATAAAATATGGCCAGCA
TTGTACTTGTTCAAGTAATTGCGATTCTATGGAACACATATATAAGTTTTAAAACTAACG
AAAATACATCACCAAATGGTGATTATAATGCAAGATTATAA

>g11645.t46 Gene=g11645 Length=145
MLSQIARIYQNGVSKYPYLAQGIQTAVLMSTGDIIAQKVVEKKASIDYKRNGNFLLIGFV
GGLGLRKWYGFLSNSIKGNNKAIIAVKKVGVDQLVFAPIFIGVFISAVGMLQGSKPNEIK
KKLEREYPDILKANYKIWPALYLFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g11645.t46 PANTHER PTHR11266 PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 6 140 6.5E-27
1 g11645.t46 Pfam PF04117 Mpv17 / PMP22 family 109 142 1.8E-6
6 g11645.t46 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 51 -
9 g11645.t46 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 69 -
7 g11645.t46 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 70 88 -
8 g11645.t46 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -
5 g11645.t46 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 112 145 -
4 g11645.t46 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 69 -
3 g11645.t46 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -

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