General information for g949.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peroxisomal membrane protein 11C.
Parent gene
- The parent gene g949 is located on chr_3: 7018446..7020504 (+ 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_3 | g949 | g949.t1 | TSS | g949.t1 | 7016912 | 7016912 |
| chr_3 | g949 | g949.t1 | isoform | g949.t1 | 7016957 | 7018446 |
| chr_3 | g949 | g949.t1 | exon | g949.t1.exon1 | 7016957 | 7017019 |
| chr_3 | g949 | g949.t1 | cds | g949.t1.CDS1 | 7016957 | 7017019 |
| chr_3 | g949 | g949.t1 | exon | g949.t1.exon2 | 7017504 | 7017871 |
| chr_3 | g949 | g949.t1 | cds | g949.t1.CDS2 | 7017504 | 7017871 |
| chr_3 | g949 | g949.t1 | exon | g949.t1.exon3 | 7018164 | 7018446 |
| chr_3 | g949 | g949.t1 | cds | g949.t1.CDS3 | 7018164 | 7018446 |
| chr_3 | g949 | g949.t1 | TTS | g949.t1 | 7018694 | 7018694 |
Sequences
>g949.t1 Gene=g949 Length=714
ATGCCAAATCATATTTTAGGGGAAATTTGCTCAATGCTTGACACTTACACAGGTCGAGAC
AAAATTGTTCGAACATTATGTTATACGGCAAAATTAATGTCTGCAATTCAAGCTGAGAAA
GGTAACGATGATTATGCCAAAAAATTTGCAATTTTTAGTACGAAGATGTCCCAAACACGT
GCAAACTTGAGATTATTTGATGACATTCCAATGATTCAATACTCGCTTGAATATGGTTTA
GGAGAAAAGGAACCTGATCGAATGATGGCAATGATTGGTGTAATTACAAATATTGTAGAT
CATTTGTATTATCCTGTAGATAAAATTTGTTGGGCCATTGATTCAAAAATTTTGAATCCA
AAGAACCCAGAAAAATGGGACACTTTAAACAGTGTGTTTTGGGCGGCATCAATTTATTTG
AACCTAATGAAGACTATTAGACTTGTTTACATCATGCGTCTTCATCGGCAAAATATTGAT
AAAATAGAAAATGAGAGTGCTGTTGCTTTGAAGAAGCTCGAAGCAAAGGAACGAATGGAA
ATGATTAGTATTTTTAGACTTACACTTGATTTTGTTCATGCTTCATCAACCCTTCCGTCC
GGCTGGCTTTGGGGTGGAAAATTATCTACATTTTCAGTTGGACTCATAGGTAGCACTTCC
TCGTTAATTGGTCTTTATCAGTATTTTGCAAAGAAGCGACTTGCGAAAAGTTAA
>g949.t1 Gene=g949 Length=237
MPNHILGEICSMLDTYTGRDKIVRTLCYTAKLMSAIQAEKGNDDYAKKFAIFSTKMSQTR
ANLRLFDDIPMIQYSLEYGLGEKEPDRMMAMIGVITNIVDHLYYPVDKICWAIDSKILNP
KNPEKWDTLNSVFWAASIYLNLMKTIRLVYIMRLHRQNIDKIENESAVALKKLEAKERME
MISIFRLTLDFVHASSTLPSGWLWGGKLSTFSVGLIGSTSSLIGLYQYFAKKRLAKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g949.t1 | Coils | Coil | Coil | 159 | 179 | - |
| 2 | g949.t1 | PANTHER | PTHR20990 | PEROXISOMAL BIOGENESIS FACTOR 11 | 5 | 232 | 1.1E-76 |
| 1 | g949.t1 | Pfam | PF05648 | Peroxisomal biogenesis factor 11 (PEX11) | 8 | 228 | 2.6E-49 |
| 8 | g949.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 131 | - |
| 11 | g949.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 132 | 152 | - |
| 5 | g949.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 153 | 183 | - |
| 9 | g949.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 184 | 204 | - |
| 7 | g949.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 205 | 209 | - |
| 10 | g949.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 229 | - |
| 6 | g949.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 230 | 237 | - |
| 3 | g949.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 208 | 230 | - |
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 K13353 (peroxin-11C)
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.
