Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t7 TTS g10087.t7 7317069 7317069
chr_1 g10087 g10087.t7 isoform g10087.t7 7317247 7318822
chr_1 g10087 g10087.t7 exon g10087.t7.exon1 7317247 7317924
chr_1 g10087 g10087.t7 cds g10087.t7.CDS1 7317247 7317924
chr_1 g10087 g10087.t7 exon g10087.t7.exon2 7317990 7318090
chr_1 g10087 g10087.t7 cds g10087.t7.CDS2 7317990 7318090
chr_1 g10087 g10087.t7 exon g10087.t7.exon3 7318197 7318252
chr_1 g10087 g10087.t7 cds g10087.t7.CDS3 7318197 7318252
chr_1 g10087 g10087.t7 exon g10087.t7.exon4 7318392 7318456
chr_1 g10087 g10087.t7 cds g10087.t7.CDS4 7318392 7318456
chr_1 g10087 g10087.t7 exon g10087.t7.exon5 7318619 7318822
chr_1 g10087 g10087.t7 cds g10087.t7.CDS5 7318619 7318666
chr_1 g10087 g10087.t7 TSS g10087.t7 NA NA

Sequences

>g10087.t7 Gene=g10087 Length=1104
TTTTAATTTAAAATTAATTGTTCAAGAAAAGAAAATTACAATAATTTTTCCAATACAACA
AATTGTAAACATTGTAGAATTGTAGAATTGTAAACAGTATTTTTTCGAATTTAATGTCCT
CAAAACTTGTAATATTTGAAAAATAAAGGAAATACAATGATGATAATCAATATAAACTTA
AAACCATTGGCTGTTTATCTATTTGAAGCATTATCAAATTTGTTTTCATATCACCTTTTT
GTTCATGCTACAAGTGGAAGTTGTGCCAGTCTCGTTGCAGTCGCAGCAGTTTATCCATTT
CTAACAATTCTACAAAGAAAGCAGTTGGATGACTTGAAAGCAGTTAGACATCTAAATTCA
TTTGAGCTAATTTATTATTTATTCAAAAAAGAAGGCTTAGGTTCAATTTATCGAGGACTG
ATTCCAGTAATGCAAAGTAGTTGCATCAGCAACTTTGTATATTTCTATGTTTTTCATTTA
TTGAAAAGCTTCAAAACCAGAGATGCTCAATCAGCAGGGTCAGATTTAATACTCGGAACA
TTAGCTGGTTGCATTAATGTATTAACCACCACTCCACTTTGGTGTGTAAATACAAGACTA
AGAATGAACAATATTAACTACTCTCTCCCTTATGACAATCTCATATCTGGTCTCAAATAT
ATTGCCAAGAATGAGGGAATTGAAAAATTATGGGCTGGTACTCAAGCATCTCTATTACTC
TCTATTAACCCTGCTATACAATTTTCAGTTTATGAGTCAATCAAGCGCTACTTGACAAAA
CTATATGGACAAGAAAAACCTTCTGTATTTTATTTTTTCTTTCTCGGAGCCTTATCTAAA
GTCATTTCAACCTGCATAACTTATCCACTGCAATTAGTACAAACAAAAATGAGATATGGT
GATAAAAATAACACAAATGAAATGGGTACTATGGAATTGCTTTTACAAATTATCAAAACC
AATGGATTTAAAGGATTATATGTTGGAATGGAAGCGAAATTTCTACAGACCATATTAACA
GCTGCACTCATGTTTTTGGCTTATGAAAAGATTGCTCGATTTGTGAAAATTTTGTTGAGA
GCATCAGCAGCTTCGACAACTTAA

>g10087.t7 Gene=g10087 Length=315
MMIININLKPLAVYLFEALSNLFSYHLFVHATSGSCASLVAVAAVYPFLTILQRKQLDDL
KAVRHLNSFELIYYLFKKEGLGSIYRGLIPVMQSSCISNFVYFYVFHLLKSFKTRDAQSA
GSDLILGTLAGCINVLTTTPLWCVNTRLRMNNINYSLPYDNLISGLKYIAKNEGIEKLWA
GTQASLLLSINPAIQFSVYESIKRYLTKLYGQEKPSVFYFFFLGALSKVISTCITYPLQL
VQTKMRYGDKNNTNEMGTMELLLQIIKTNGFKGLYVGMEAKFLQTILTAALMFLAYEKIA
RFVKILLRASAASTT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10087.t7 Gene3D G3DSA:1.50.40.10 Mitochondrial carrier domain 27 312 9.2E-53
4 g10087.t7 PANTHER PTHR45939:SF5 PEROXISOMAL MEMBRANE PROTEIN PMP34 18 312 2.3E-95
5 g10087.t7 PANTHER PTHR45939 PEROXISOMAL MEMBRANE PROTEIN PMP34-RELATED 18 312 2.3E-95
1 g10087.t7 Pfam PF00153 Mitochondrial carrier protein 26 113 1.1E-10
3 g10087.t7 Pfam PF00153 Mitochondrial carrier protein 119 208 1.1E-17
2 g10087.t7 Pfam PF00153 Mitochondrial carrier protein 216 303 4.3E-17
19 g10087.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 26 -
23 g10087.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 27 49 -
16 g10087.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 50 83 -
26 g10087.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 84 104 -
20 g10087.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 105 123 -
25 g10087.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 124 144 -
18 g10087.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 145 216 -
22 g10087.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 217 238 -
21 g10087.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 239 281 -
24 g10087.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 282 299 -
17 g10087.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 300 315 -
14 g10087.t7 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 25 112 15.348
15 g10087.t7 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 118 205 17.836
13 g10087.t7 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 215 302 18.201
11 g10087.t7 SUPERFAMILY SSF103506 Mitochondrial carrier 26 298 4.05E-56
7 g10087.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 27 49 -
6 g10087.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 87 109 -
10 g10087.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 124 146 -
9 g10087.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 217 239 -
8 g10087.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 274 296 -

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

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