General information for g4552.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peroxisomal membrane protein 11B.
Parent gene
- The parent gene g4552 is located on chr_2: 3215481..3216429 (+ 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 | g4552 | g4552.t1 | TSS | g4552.t1 | 3215205 | 3215205 |
| chr_2 | g4552 | g4552.t1 | isoform | g4552.t1 | 3215239 | 3216031 |
| chr_2 | g4552 | g4552.t1 | exon | g4552.t1.exon1 | 3215239 | 3215413 |
| chr_2 | g4552 | g4552.t1 | cds | g4552.t1.CDS1 | 3215239 | 3215413 |
| chr_2 | g4552 | g4552.t1 | exon | g4552.t1.exon2 | 3215475 | 3216031 |
| chr_2 | g4552 | g4552.t1 | cds | g4552.t1.CDS2 | 3215475 | 3216031 |
| chr_2 | g4552 | g4552.t1 | TTS | g4552.t1 | 3216422 | 3216422 |
Sequences
>g4552.t1 Gene=g4552 Length=732
ATGGATATAGTTATTAAGTTAAATAGTCAAGTTGCGGGTAAAGATAAAGTAGCAAGACTC
ATACAGTACTCATGTAGAGCATTATGGGATTCACTAAACCAAAAAGATGAATCACAGATA
GCATTAATTCATCAACTTAAAAATTTAGAATTTATACTGTCATCATTCCGCAAACTATTA
CGCTTTGGAAAAAGTTTCGAAGTTTTCTACAGTTCACTCAAATCGATACATTATAGTGAT
GCATGGATTGCTTTCACATCAACAGTCACAAAAATTTGCCAAGCAATTTTTCTACTTACT
GATCATATAATTTGGCTATCGAGAAGTGGTTTATTTAAAAATATTGATACACCTAAATGG
AGTCAAAGAAGTAATAGATATTGGGTTGTTTCACTCATTATGAGCATCATAAGGGATGTT
TATGAAATAAATCGTGTCATTTCAAGTTTTACATCATATAAAGACCTCACACAATGCATT
GCATCATCAATGTTCAGCATAAGAAGTACAAAAGACATCACACGATGTGCATCATCATTG
GCTGAGTTTCTTGTCACTTATAAGCATATAACGATAGACACCATCAAAAATGTCTGTGAT
CTATTCATTCCACTAAATGGTCTAGGATATACAAAATTATCGCCTAAGGTTATTGGCCTA
TTAGGCGTTATATCGTCATTAATGGGTCTCATTGTTGTTCTCGATCCAAGCTGTAAATTA
CTTCCTCAATGA
>g4552.t1 Gene=g4552 Length=243
MDIVIKLNSQVAGKDKVARLIQYSCRALWDSLNQKDESQIALIHQLKNLEFILSSFRKLL
RFGKSFEVFYSSLKSIHYSDAWIAFTSTVTKICQAIFLLTDHIIWLSRSGLFKNIDTPKW
SQRSNRYWVVSLIMSIIRDVYEINRVISSFTSYKDLTQCIASSMFSIRSTKDITRCASSL
AEFLVTYKHITIDTIKNVCDLFIPLNGLGYTKLSPKVIGLLGVISSLMGLIVVLDPSCKL
LPQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4552.t1 | PANTHER | PTHR12652 | PEROXISOMAL BIOGENESIS FACTOR 11 | 2 | 231 | 2.4E-40 |
| 1 | g4552.t1 | Pfam | PF05648 | Peroxisomal biogenesis factor 11 (PEX11) | 1 | 231 | 1.2E-56 |
| 3 | g4552.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 216 | - |
| 5 | g4552.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 217 | 234 | - |
| 4 | g4552.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 235 | 243 | - |
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:0005779 | integral component of peroxisomal membrane | CC |
| GO:0016559 | peroxisome fission | BP |
KEGG
Orthology
- This transcript has been annotated with K13352 (peroxin-11B)
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.
