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.t2 isoform g13238.t2 28733273 28734358
chr_1 g13238 g13238.t2 exon g13238.t2.exon1 28733273 28733533
chr_1 g13238 g13238.t2 cds g13238.t2.CDS1 28733273 28733533
chr_1 g13238 g13238.t2 exon g13238.t2.exon2 28733592 28733647
chr_1 g13238 g13238.t2 cds g13238.t2.CDS2 28733592 28733647
chr_1 g13238 g13238.t2 exon g13238.t2.exon3 28733722 28733909
chr_1 g13238 g13238.t2 cds g13238.t2.CDS3 28733722 28733909
chr_1 g13238 g13238.t2 exon g13238.t2.exon4 28734270 28734358
chr_1 g13238 g13238.t2 cds g13238.t2.CDS4 28734270 28734358
chr_1 g13238 g13238.t2 TSS g13238.t2 NA NA
chr_1 g13238 g13238.t2 TTS g13238.t2 NA NA

Sequences

>g13238.t2 Gene=g13238 Length=594
ATGTTCGGAAGAAATAATAGTGAACCACTATGGAAAATTTTTAGAAAGCACCCTATAACA
AGAGGAATGGCATCCTATCTAGTCATATGGCCAACTGCAAATATTATACAACAGACATTA
TGTGAGAAGGATTTTGATTGGTGGAAGGTAGTACGATTTGGATTATATGGATGTTTTATC
ACAGCACCAAGTCTATATTGTTGGGTTAAACTTGCTACATTCATGTATCCAAATAATCAA
CTTCGTCTATGCATGGCTAAAGCACTAATCGAACAAATATCATACACACCACTTGCTATG
TGCACGTTTTTTTATAGTATGACATGGTTAGAAACTTTTTCAGCAGCTGAAGCTTTTCAA
GAAGTAAAAGTGAAATTTCCACCAACTTATTTTACTGCTATTACAATTTGGCCTCTAATT
GGCACCATAAACTTTGCATTCGTACCTGAAAGAAATCGCGTACTTTTTACCTCATGCTTT
TCATTGTTGTGGACGATATATTTAGCTCATATGAAAAACAGACAACGTGATAAGATGCTC
TTGGATAAAAATAATAAATCAAATGAGCTCACAACGAATACAAAAGACAAATAA

>g13238.t2 Gene=g13238 Length=197
MFGRNNSEPLWKIFRKHPITRGMASYLVIWPTANIIQQTLCEKDFDWWKVVRFGLYGCFI
TAPSLYCWVKLATFMYPNNQLRLCMAKALIEQISYTPLAMCTFFYSMTWLETFSAAEAFQ
EVKVKFPPTYFTAITIWPLIGTINFAFVPERNRVLFTSCFSLLWTIYLAHMKNRQRDKML
LDKNNKSNELTTNTKDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13238.t2 PANTHER PTHR11266 PEROXISOMAL MEMBRANE PROTEIN 2, PXMP2 MPV17 12 178 1.0E-64
3 g13238.t2 PANTHER PTHR11266:SF75 IP10007P 12 178 1.0E-64
1 g13238.t2 Pfam PF04117 Mpv17 / PMP22 family 110 168 6.1E-17
12 g13238.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 52 -
14 g13238.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 76 -
9 g13238.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 77 87 -
16 g13238.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 110 -
11 g13238.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 129 -
13 g13238.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 147 -
8 g13238.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 148 153 -
15 g13238.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 171 -
10 g13238.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 172 197 -
6 g13238.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 72 -
5 g13238.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -
4 g13238.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 130 147 -
7 g13238.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 154 171 -

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. There were no conditions that were differentially expressed