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.t14 TSS g13237.t14 28731447 28731447
chr_1 g13237 g13237.t14 isoform g13237.t14 28731877 28732519
chr_1 g13237 g13237.t14 exon g13237.t14.exon1 28731877 28732040
chr_1 g13237 g13237.t14 cds g13237.t14.CDS1 28731891 28732040
chr_1 g13237 g13237.t14 exon g13237.t14.exon2 28732100 28732519
chr_1 g13237 g13237.t14 cds g13237.t14.CDS2 28732100 28732519
chr_1 g13237 g13237.t14 TTS g13237.t14 28732729 28732729

Sequences

>g13237.t14 Gene=g13237 Length=584
TTCGTGCTCATCCAATGTTGAAAGGTATGGCCGTTTATGCATTTATCTGGCCAACAAGTG
CAAGCATACAGCAATTGATCAATAAAGAAGAATTTGATTGGAAGAAATGCTTTAGATTCT
TTCTTTTTGGAACATTTTTTGTAGCTCCATCACTTTACGGATGGGTTCATCTGTCATCGA
ACATGTGGAGTGAAATGACTTTAAAAACAGGGATTACAAAAGCTGTTGTTGAACAATTTT
CTTATGGACCAGCTGCAAGTGTGAGTTTTTTTACAATCATGACTTTGCTTGAAGGACGAT
CATTCTCAGAAGCTAAAATGGAAGTTAGAGAGAAATTTCCTCAAACTTTTCAAGTGGGAG
TTTGTTTTTGGCCATTTTTCCAAATTATCAATTTTACGTTTATTAAAGAACGAAATCGTG
TACCTTTCGTAGCATTTGGTAGCTTTATATGGACAATATTTCTTGCTTACATGAAAACAC
TTGATACACAAAAATTACATGAAGTTCATGTTCAAGAACATGAACATCCTACACATACGT
TCTTTGAAAAGCTTAAAATAAACTTGCAAATCGGTACAGAATAA

>g13237.t14 Gene=g13237 Length=189
MLKGMAVYAFIWPTSASIQQLINKEEFDWKKCFRFFLFGTFFVAPSLYGWVHLSSNMWSE
MTLKTGITKAVVEQFSYGPAASVSFFTIMTLLEGRSFSEAKMEVREKFPQTFQVGVCFWP
FFQIINFTFIKERNRVPFVAFGSFIWTIFLAYMKTLDTQKLHEVHVQEHEHPTHTFFEKL
KINLQIGTE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13237.t14 PANTHER PTHR11266 PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 1 160 1.4E-65
3 g13237.t14 PANTHER PTHR11266:SF75 IP10007P 1 160 1.4E-65
1 g13237.t14 Pfam PF04117 Mpv17 / PMP22 family 91 150 1.2E-18
11 g13237.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
17 g13237.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 23 -
9 g13237.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 24 34 -
15 g13237.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 35 55 -
12 g13237.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 56 74 -
18 g13237.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 75 92 -
10 g13237.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 93 111 -
16 g13237.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 130 -
13 g13237.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 131 135 -
14 g13237.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 136 153 -
8 g13237.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 154 189 -
5 g13237.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 32 54 -
4 g13237.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 75 97 -
7 g13237.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 112 129 -
6 g13237.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 136 153 -

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