General information for g5043.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5043 is located on chr_2: 6594368..6595766 (+ 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_2 | g5043 | g5043.t2 | TSS | g5043.t2 | 6594122 | 6594122 |
| chr_2 | g5043 | g5043.t2 | isoform | g5043.t2 | 6594368 | 6594976 |
| chr_2 | g5043 | g5043.t2 | exon | g5043.t2.exon1 | 6594368 | 6594491 |
| chr_2 | g5043 | g5043.t2 | cds | g5043.t2.CDS1 | 6594368 | 6594491 |
| chr_2 | g5043 | g5043.t2 | exon | g5043.t2.exon2 | 6594606 | 6594976 |
| chr_2 | g5043 | g5043.t2 | cds | g5043.t2.CDS2 | 6594606 | 6594976 |
| chr_2 | g5043 | g5043.t2 | TTS | g5043.t2 | 6595975 | 6595975 |
Sequences
>g5043.t2 Gene=g5043 Length=495
ATGACTTTAGACTCAACAACGCTGCCCTTGGCAAATGGTTATGCACCTGTTAATTATCGA
CAACAAGTAAATATGGGCGGTAGTGATGTATTCGGTGGACCTTATCAAATTCAGACACCA
TCAGGCATTGTGCACTCAACACAGCCATCAGCACAAATTACACCTCCACCACTGCCGCCA
CGACCGAATTCATATTTACAATCATCATCATCATCCATGTTTTCACCTTATGGCAATAAT
TATGGCTTCAATTCATTTGGTGGTGGATTTAATTCGAATTATGGTTATGGCATGGGCGGA
TTCAATTCTTTTAATTCATTTGGAGGTTTTGGAAGTGGATACGGAAGACCATTTGGCAAT
CCATTAGATCCAGAAATGAGATTTATACAAATGGCAGAAGAAAGTTCACGATCAACATTT
CAAAGTATTGAGTCAGTTGTATCAACTATTGGAAATATTGCAACTATGCTTGATAGTACT
TATTTTGCATTAACA
>g5043.t2 Gene=g5043 Length=165
MTLDSTTLPLANGYAPVNYRQQVNMGGSDVFGGPYQIQTPSGIVHSTQPSAQITPPPLPP
RPNSYLQSSSSSMFSPYGNNYGFNSFGGGFNSNYGYGMGGFNSFNSFGGFGSGYGRPFGN
PLDPEMRFIQMAEESSRSTFQSIESVVSTIGNIATMLDSTYFALT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5043.t2 | PANTHER | PTHR19332 | PEROXISOMAL MEMBRANE PROTEIN PEX13 | 40 | 164 | 0 |
| 3 | g5043.t2 | PANTHER | PTHR19332:SF1 | PEROXISOMAL MEMBRANE PROTEIN PEX13 | 40 | 164 | 0 |
| 1 | g5043.t2 | Pfam | PF04088 | Peroxin 13, N-terminal region | 127 | 164 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5043/g5043.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5043.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016560 | protein import into peroxisome matrix, docking | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0005777 | peroxisome | CC |
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.
