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.t5 TTS g10087.t5 7317069 7317069
chr_1 g10087 g10087.t5 isoform g10087.t5 7317247 7318471
chr_1 g10087 g10087.t5 exon g10087.t5.exon1 7317247 7317901
chr_1 g10087 g10087.t5 cds g10087.t5.CDS1 7317247 7317747
chr_1 g10087 g10087.t5 exon g10087.t5.exon2 7317966 7318090
chr_1 g10087 g10087.t5 exon g10087.t5.exon3 7318197 7318252
chr_1 g10087 g10087.t5 exon g10087.t5.exon4 7318392 7318471
chr_1 g10087 g10087.t5 TSS g10087.t5 7318538 7318538

Sequences

>g10087.t5 Gene=g10087 Length=916
ATGTCTAATTCAAAGGAAGCATTATCAAATTTGTTTTCATATCACCTTTTTGTTCATGCT
ACAAGTGGAAGTTGTGCCAGTCTCGTTGCAGTCGCAGCAGTTTATCCATTTCTAACAATT
CTACAAAGAAAGCAGTTGGATGACTTGAAAGCAGTTAGACATCTAAATTCATTTGAGCTA
ATTTATTATTTATTCAAAAAAGAAGGCTTAGGTTCAATTTATCGAGGACTGATTCCAGTA
ATGCAATAATTAATATTGATACAACTTTGTATATTTCTATGTTTTTCATTTATTGAAAAG
CTTCAAAACCAGAGATGCTCAATCAGCAGGGTCAGATTTAATACTCGGAACATTAGCTGG
TTGCATTAATGTATTAACCACCACTCCACTTTGGTGTGTAAATACAAGACTAAGAATGAA
CAATATTAACTACTCTCTCCCTTATGACAATCTCATATCTGGTCTCAAATATATTGCCAA
GAATGAGGGAATTGAAAAATTATGGGCTGGTACTCAAGCATCTCTATTACTCTCTATTAA
CCCTGCTATACAATTTTCAGTTTATGAGTCAATCAAGCGCTACTTGACAAAACTATATGG
ACAAGAAAAACCTTCTGTATTTTATTTTTTCTTTCTCGGAGCCTTATCTAAAGTCATTTC
AACCTGCATAACTTATCCACTGCAATTAGTACAAACAAAAATGAGATATGGTGATAAAAA
TAACACAAATGAAATGGGTACTATGGAATTGCTTTTACAAATTATCAAAACCAATGGATT
TAAAGGATTATATGTTGGAATGGAAGCGAAATTTCTACAGACCATATTAACAGCTGCACT
CATGTTTTTGGCTTATGAAAAGATTGCTCGATTTGTGAAAATTTTGTTGAGAGCATCAGC
AGCTTCGACAACTTAA

>g10087.t5 Gene=g10087 Length=166
MNNINYSLPYDNLISGLKYIAKNEGIEKLWAGTQASLLLSINPAIQFSVYESIKRYLTKL
YGQEKPSVFYFFFLGALSKVISTCITYPLQLVQTKMRYGDKNNTNEMGTMELLLQIIKTN
GFKGLYVGMEAKFLQTILTAALMFLAYEKIARFVKILLRASAASTT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10087.t5 Gene3D G3DSA:1.50.40.10 Mitochondrial carrier domain 2 157 2.5E-31
3 g10087.t5 PANTHER PTHR45939:SF5 PEROXISOMAL MEMBRANE PROTEIN PMP34 9 163 1.5E-51
4 g10087.t5 PANTHER PTHR45939 PEROXISOMAL MEMBRANE PROTEIN PMP34-RELATED 9 163 1.5E-51
2 g10087.t5 Pfam PF00153 Mitochondrial carrier protein 11 59 6.2E-8
1 g10087.t5 Pfam PF00153 Mitochondrial carrier protein 67 154 1.0E-17
12 g10087.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 67 -
13 g10087.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 89 -
11 g10087.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 90 166 -
9 g10087.t5 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 1 56 11.486
10 g10087.t5 ProSiteProfiles PS50920 Solute carrier (Solcar) repeat profile. 66 153 18.201
7 g10087.t5 SUPERFAMILY SSF103506 Mitochondrial carrier 8 149 3.14E-31
6 g10087.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 90 -
5 g10087.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 125 147 -

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