General information for g15541.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Signal peptidase complex subunit 3.
Parent gene
- The parent gene g15541 is located on chr_4: 5798732..5806205 (+ 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_4 | g15541 | g15541.t1 | TSS | g15541.t1 | 5798641 | 5798641 |
| chr_4 | g15541 | g15541.t1 | isoform | g15541.t1 | 5798732 | 5799327 |
| chr_4 | g15541 | g15541.t1 | exon | g15541.t1.exon1 | 5798732 | 5799037 |
| chr_4 | g15541 | g15541.t1 | cds | g15541.t1.CDS1 | 5798732 | 5799037 |
| chr_4 | g15541 | g15541.t1 | exon | g15541.t1.exon2 | 5799094 | 5799327 |
| chr_4 | g15541 | g15541.t1 | cds | g15541.t1.CDS2 | 5799094 | 5799327 |
| chr_4 | g15541 | g15541.t1 | TTS | g15541.t1 | 5799421 | 5799421 |
Sequences
>g15541.t1 Gene=g15541 Length=540
ATGCACACAGTTCTCACAAGAGGTAATGCTATTCTAGCGTACACATTAAGCGTTCTTGCC
TGCCTAACATTCTGTTGCTTCGTGTCGACCGTCTTTCTTGATTATCGCACAAATGTTAAA
ATAAATGCGGTAAAGACGCTGGTAAAAAATGTTCCAAACTATGGAAACAACAAAGAACTC
AACGATTTGGGCTTCATAACATTCGATTTGCAGACTGATCTGAGTGGATTATTTAATTGG
AATGTGAAACAACTTTTTCTGTATTTGACTGCAGAATACAAGACTGAAAGCAATGAATTG
AATCAAGTCGTTCTTTGGGACAAAATTATTCTCCGTGGCGAAAATGCCATTTTAGATTTT
AAGAATATGAACACAAAATATTATTTCTGGGATGATGGCAATGGTCTTCGAGGGCATAAA
AATGTAACTTTAACACTCAGCTGGAACATAATACCAAATGCAGGTTTACTGCCAACACTT
TTCGGCATTGGTGAACATTCATTCAAATTTCCTGATCAATACACAATGCAACCAGTTTAG
>g15541.t1 Gene=g15541 Length=179
MHTVLTRGNAILAYTLSVLACLTFCCFVSTVFLDYRTNVKINAVKTLVKNVPNYGNNKEL
NDLGFITFDLQTDLSGLFNWNVKQLFLYLTAEYKTESNELNQVVLWDKIILRGENAILDF
KNMNTKYYFWDDGNGLRGHKNVTLTLSWNIIPNAGLLPTLFGIGEHSFKFPDQYTMQPV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g15541.t1 | PANTHER | PTHR12804:SF7 | SIGNAL PEPTIDASE COMPLEX SUBUNIT 3 | 1 | 176 | 9.8E-65 |
| 3 | g15541.t1 | PANTHER | PTHR12804 | MICROSOMAL SIGNAL PEPTIDASE 23 KD SUBUNIT SPC22/23 | 1 | 176 | 9.8E-65 |
| 9 | g15541.t1 | PIRSF | PIRSF016089 | SPC3 | 1 | 177 | 7.8E-48 |
| 1 | g15541.t1 | Pfam | PF04573 | Signal peptidase subunit | 5 | 173 | 3.6E-60 |
| 7 | g15541.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 8 | g15541.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 33 | - |
| 6 | g15541.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 34 | 179 | - |
| 5 | g15541.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 21 | 5.0 |
| 4 | g15541.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 32 | - |
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:0016021 | integral component of membrane | CC |
| GO:0006465 | signal peptide processing | BP |
| GO:0005787 | signal peptidase complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12948 (signal peptidase complex subunit 3 [EC:3.4.-.-])
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.
