Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Peroxisomal membrane protein PMP34.

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 g10087 g10087.t2 TTS g10087.t2 7317069 7317069
chr_1 g10087 g10087.t2 isoform g10087.t2 7317247 7318090
chr_1 g10087 g10087.t2 exon g10087.t2.exon1 7317247 7318090
chr_1 g10087 g10087.t2 cds g10087.t2.CDS1 7317247 7317921
chr_1 g10087 g10087.t2 TSS g10087.t2 7318095 7318095

Sequences

>g10087.t2 Gene=g10087 Length=844
TGGATGACTTGAAAGCAGTTAGACATCTAAATTCATTTGAGCTAATTTATTATTTATTCA
AAAAAGAAGGCTTAGGTTCAATTTATCGAGGACTGATTCCAGTAATGCAATAATTAATAT
TGATAGTGCTATTTCTAATTATTTAATATTTCATTCGCGATCATAGGTAATGCAAAGTAG
TTGCATCAGCAACTTTGTATATTTCTATGTTTTTCATTTATTGAAAAGCTTCAAAACCAG
AGATGCTCAATCAGCAGGGTCAGATTTAATACTCGGAACATTAGCTGGTTGCATTAATGT
ATTAACCACCACTCCACTTTGGTGTGTAAATACAAGACTAAGAATGAACAATATTAACTA
CTCTCTCCCTTATGACAATCTCATATCTGGTCTCAAATATATTGCCAAGAATGAGGGAAT
TGAAAAATTATGGGCTGGTACTCAAGCATCTCTATTACTCTCTATTAACCCTGCTATACA
ATTTTCAGTTTATGAGTCAATCAAGCGCTACTTGACAAAACTATATGGACAAGAAAAACC
TTCTGTATTTTATTTTTTCTTTCTCGGAGCCTTATCTAAAGTCATTTCAACCTGCATAAC
TTATCCACTGCAATTAGTACAAACAAAAATGAGATATGGTGATAAAAATAACACAAATGA
AATGGGTACTATGGAATTGCTTTTACAAATTATCAAAACCAATGGATTTAAAGGATTATA
TGTTGGAATGGAAGCGAAATTTCTACAGACCATATTAACAGCTGCACTCATGTTTTTGGC
TTATGAAAAGATTGCTCGATTTGTGAAAATTTTGTTGAGAGCATCAGCAGCTTCGACAAC
TTAA

>g10087.t2 Gene=g10087 Length=224
MQSSCISNFVYFYVFHLLKSFKTRDAQSAGSDLILGTLAGCINVLTTTPLWCVNTRLRMN
NINYSLPYDNLISGLKYIAKNEGIEKLWAGTQASLLLSINPAIQFSVYESIKRYLTKLYG
QEKPSVFYFFFLGALSKVISTCITYPLQLVQTKMRYGDKNNTNEMGTMELLLQIIKTNGF
KGLYVGMEAKFLQTILTAALMFLAYEKIARFVKILLRASAASTT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10087.t2 Coils Coil Coil 220 224 -
6 g10087.t2 Gene3D G3DSA:1.50.40.10 Mitochondrial carrier domain 1 215 1.7E-42
3 g10087.t2 PANTHER PTHR45939:SF5 PEROXISOMAL MEMBRANE PROTEIN PMP34 3 221 1.4E-75
4 g10087.t2 PANTHER PTHR45939 PEROXISOMAL MEMBRANE PROTEIN PMP34-RELATED 3 221 1.4E-75
2 g10087.t2 Pfam PF00153 Mitochondrial carrier protein 28 117 5.5E-18
1 g10087.t2 Pfam PF00153 Mitochondrial carrier protein 125 212 2.1E-17
11 g10087.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 32 -
13 g10087.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 33 53 -
8 g10087.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 54 125 -
14 g10087.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 126 147 -
10 g10087.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 148 190 -
12 g10087.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 191 208 -
9 g10087.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 209 224 -
18 g10087.t2 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 27 114 17.836
19 g10087.t2 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 124 211 18.201
5 g10087.t2 SUPERFAMILY SSF103506 Mitochondrial carrier 4 207 6.54E-42
17 g10087.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 33 55 -
16 g10087.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 126 148 -
15 g10087.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 183 205 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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