General information for g10857.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peroxisomal biogenesis factor 3.
Parent gene
- The parent gene g10857 is located on chr_1: 12303938..12305534 (- strand)
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 | g10857 | g10857.t3 | TTS | g10857.t3 | 12303793 | 12303793 |
| chr_1 | g10857 | g10857.t3 | isoform | g10857.t3 | 12303938 | 12305534 |
| chr_1 | g10857 | g10857.t3 | exon | g10857.t3.exon1 | 12303938 | 12304945 |
| chr_1 | g10857 | g10857.t3 | cds | g10857.t3.CDS1 | 12303938 | 12304945 |
| chr_1 | g10857 | g10857.t3 | exon | g10857.t3.exon2 | 12305028 | 12305173 |
| chr_1 | g10857 | g10857.t3 | cds | g10857.t3.CDS2 | 12305028 | 12305153 |
| chr_1 | g10857 | g10857.t3 | exon | g10857.t3.exon3 | 12305242 | 12305534 |
| chr_1 | g10857 | g10857.t3 | TSS | g10857.t3 | NA | NA |
Sequences
>g10857.t3 Gene=g10857 Length=1447
TGACAATTGTTTAAAATTTAAATTCCAATTATTTTTTTTCAATTTCTAAAAATATTGATT
TTTCACTTTCTTGCTTACACTATTTTGCTCCAAGGGATTATAAATAAATGTACATTTTCA
AGAGGTGTCCGGCCACAAAAACAGTGCAGTCATTTTTGTTTGGATTCGATTTTAAGAAAA
TAGAAAATCGAAAACAAGTGTTTCACTTCTCATATTTGGTTTAAATTATTAATAAATGGT
GCTCTGAATAAATTTAAACTGGTCAAACATTAAAGTACAGAGCAAATAAAAGAGTGATTT
ATGAGGATTAAAAATGTTATCTAAACTAAAAAGTTTCGCCTCTCGTCATAAGAAAAAAAT
TATTGTGGGTGGAGTGATTGTTGCAGCGGGATTTGCTCTGAGATATGCTCAAAGAAAATT
AGTAGAGTATCAAGAGAAGCAAGTCAAAGAATTTTTGGAAAAAACACGTCGATTGCAGCA
TTTTGAATCAACCGAAAAGACTACAGATCAAGCTATTATTAGTCTCACAACAGGATTATG
CGAGTCTGTTTTAAAAATTTTCGATACAGAAAGTATTTTAAACGAACTTCGAACTAACAA
CCATAATGGAAAGAAAATTGAGTTATGGGATGAGCTGAAAATTCTTGCTTTTGCAAAATG
CACAACACTGGTTTACGCAATTTCATTGTTAGTTGCTAGCTTGAGAGTACAATTGAATAT
CATAGGTGGATATCTTTATAAAGATACGCTTCAGTCTACAGAGAAAATTACAAAAGATAT
TCAAACAATATATAGTTTAGTGCTCATACAACACCTAATGGGAACTGGTTTAAACACACT
TGCCAAAATAATTCGTGAAAATGTCATAAAAGTGATGAAAACTCACAGTTTGAAAGAAAA
GCTTATGCTAAATGATGTGGAACAAATATTTTGGTCAATTCAAACTTCAGTTGATAAGGA
CATAAACAAGAATTTAGTGCAATTCATTTTACCGGCAGAAGTTCATCACAATCAGCAAGA
TGAAATTTTAAATAAAATGTTGGCCGATAGTATGGATGTATTTGAATGTGGTGATTTTTT
GGAAGTATGTGAGTCAAGCATTAATAATGCTTTTGCAGTTGTGATTGATAAAATAGCAGA
CTTTTATGTGGAGCCGGAAAATGGTAAAAATAAACTCAATGATCATGAGCAAGAACCTTC
AACTTCACGTGGGACTTCAGAAAATTTGATTCTAAACAACAATGGACACGTAAACATAAA
CACTATTTCATTACCTCTTGCAAAGCTTATTCCTATACTTAATGCTTTAACATCTCAAAT
TCCCACAACAAATGCAGCTGATAACAAGTCATCAAAAAACCTTGCCAGCTCAATTACAAT
TCTTCAAAGTTTAAATCAACATCTAAAAACATTGGGTGCAAATGTTTATGAAGTTTATTC
ACACTAA
>g10857.t3 Gene=g10857 Length=377
MLSKLKSFASRHKKKIIVGGVIVAAGFALRYAQRKLVEYQEKQVKEFLEKTRRLQHFEST
EKTTDQAIISLTTGLCESVLKIFDTESILNELRTNNHNGKKIELWDELKILAFAKCTTLV
YAISLLVASLRVQLNIIGGYLYKDTLQSTEKITKDIQTIYSLVLIQHLMGTGLNTLAKII
RENVIKVMKTHSLKEKLMLNDVEQIFWSIQTSVDKDINKNLVQFILPAEVHHNQQDEILN
KMLADSMDVFECGDFLEVCESSINNAFAVVIDKIADFYVEPENGKNKLNDHEQEPSTSRG
TSENLILNNNGHVNINTISLPLAKLIPILNALTSQIPTTNAADNKSSKNLASSITILQSL
NQHLKTLGANVYEVYSH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10857.t3 | PANTHER | PTHR28080:SF1 | PEROXISOMAL BIOGENESIS FACTOR 3 | 6 | 373 | 2.3E-57 |
| 5 | g10857.t3 | PANTHER | PTHR28080 | PEROXISOMAL BIOGENESIS FACTOR 3 | 6 | 373 | 2.3E-57 |
| 1 | g10857.t3 | Pfam | PF04882 | Peroxin-3 | 8 | 97 | 3.2E-8 |
| 3 | g10857.t3 | Pfam | PF04882 | Peroxin-3 | 98 | 154 | 8.0E-11 |
| 2 | g10857.t3 | Pfam | PF04882 | Peroxin-3 | 168 | 372 | 4.0E-10 |
| 7 | g10857.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 32 | - |
| 8 | g10857.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 15 | - |
| 9 | g10857.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 16 | 27 | - |
| 10 | g10857.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 28 | 32 | - |
| 6 | g10857.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 33 | 377 | - |
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:0007031 | peroxisome organization | BP |
| GO:0005779 | integral component of peroxisomal membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K13336 (peroxin-3)
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.
