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 g13238 g13238.t3 isoform g13238.t3 28733273 28734358
chr_1 g13238 g13238.t3 exon g13238.t3.exon1 28733273 28733538
chr_1 g13238 g13238.t3 cds g13238.t3.CDS1 28733273 28733538
chr_1 g13238 g13238.t3 exon g13238.t3.exon2 28733722 28733909
chr_1 g13238 g13238.t3 cds g13238.t3.CDS2 28733722 28733909
chr_1 g13238 g13238.t3 exon g13238.t3.exon3 28734270 28734358
chr_1 g13238 g13238.t3 cds g13238.t3.CDS3 28734270 28734358
chr_1 g13238 g13238.t3 TSS g13238.t3 NA NA
chr_1 g13238 g13238.t3 TTS g13238.t3 NA NA

Sequences

>g13238.t3 Gene=g13238 Length=543
ATGTTCGGAAGAAATAATAGTGAACCACTATGGAAAATTTTTAGAAAGCACCCTATAACA
AGAGGAATGGCATCCTATCTAGTCATATGGCCAACTGCAAATATTATACAACAGACATTA
TGTGAGAAGGATTTTGATTGGTGGAAGGTAGTACGATTTGGATTATATGGATGTTTTATC
ACAGCACCAAGTCTATATTGTTGGGTTAAACTTGCTACATTCATGTATCCAAATAATCAA
CTTCGTCTATGCATGGCTAAAGTAAGTATGACATGGTTAGAAACTTTTTCAGCAGCTGAA
GCTTTTCAAGAAGTAAAAGTGAAATTTCCACCAACTTATTTTACTGCTATTACAATTTGG
CCTCTAATTGGCACCATAAACTTTGCATTCGTACCTGAAAGAAATCGCGTACTTTTTACC
TCATGCTTTTCATTGTTGTGGACGATATATTTAGCTCATATGAAAAACAGACAACGTGAT
AAGATGCTCTTGGATAAAAATAATAAATCAAATGAGCTCACAACGAATACAAAAGACAAA
TAA

>g13238.t3 Gene=g13238 Length=180
MFGRNNSEPLWKIFRKHPITRGMASYLVIWPTANIIQQTLCEKDFDWWKVVRFGLYGCFI
TAPSLYCWVKLATFMYPNNQLRLCMAKVSMTWLETFSAAEAFQEVKVKFPPTYFTAITIW
PLIGTINFAFVPERNRVLFTSCFSLLWTIYLAHMKNRQRDKMLLDKNNKSNELTTNTKDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13238.t3 PANTHER PTHR11266 PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 12 88 2.8E-49
4 g13238.t3 PANTHER PTHR11266:SF75 IP10007P 12 88 2.8E-49
3 g13238.t3 PANTHER PTHR11266 PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 89 161 2.8E-49
5 g13238.t3 PANTHER PTHR11266:SF75 IP10007P 89 161 2.8E-49
1 g13238.t3 Pfam PF04117 Mpv17 / PMP22 family 93 151 5.1E-17
11 g13238.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 52 -
13 g13238.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 76 -
10 g13238.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 77 112 -
15 g13238.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 131 -
12 g13238.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 132 136 -
14 g13238.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 137 153 -
9 g13238.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 154 180 -
6 g13238.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 53 75 -
8 g13238.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 111 130 -
7 g13238.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 137 154 -

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