General information for g4118.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g4118 is located on chr_3: 30725858..30726196 (+ 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 | g4118 | g4118.t1 | TSS | g4118.t1 | 30725786 | 30725786 |
| chr_3 | g4118 | g4118.t1 | isoform | g4118.t1 | 30725858 | 30726196 |
| chr_3 | g4118 | g4118.t1 | exon | g4118.t1.exon1 | 30725858 | 30725881 |
| chr_3 | g4118 | g4118.t1 | cds | g4118.t1.CDS1 | 30725858 | 30725881 |
| chr_3 | g4118 | g4118.t1 | exon | g4118.t1.exon2 | 30725939 | 30726196 |
| chr_3 | g4118 | g4118.t1 | cds | g4118.t1.CDS2 | 30725939 | 30726196 |
| chr_3 | g4118 | g4118.t1 | TTS | g4118.t1 | 30727117 | 30727117 |
Sequences
>g4118.t1 Gene=g4118 Length=282
ATGTTTAACATTCAAACTCATATGGACTTTGAAGGCCAAAATAGAGCCGAAAAAATTTCA
CGAGCGATAATTACATTCTTTGGGTTTGCCGGACTCATTTGGGGAGCAATAATACAGCAA
TTTTCTCAAACAATTTATATTCTTGCTGCAGGCTTTGTATTGGCTTTATTAATTACCATT
CCACCTTATCCCCTTTACAGAAGAAAACCACTTAATTGGCAAAAATCAAAGAATCAAAAC
TCTGAAGGAGGCGAAAGTTCAAAGAAAAACAAACAAAAATAA
>g4118.t1 Gene=g4118 Length=93
MFNIQTHMDFEGQNRAEKISRAIITFFGFAGLIWGAIIQQFSQTIYILAAGFVLALLITI
PPYPLYRRKPLNWQKSKNQNSEGGESSKKNKQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4118.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 74 | 93 | - |
| 2 | g4118.t1 | PANTHER | PTHR13202:SF0 | SIGNAL PEPTIDASE COMPLEX SUBUNIT 1 | 3 | 91 | 8.3E-27 |
| 3 | g4118.t1 | PANTHER | PTHR13202 | MICROSOMAL SIGNAL PEPTIDASE 12 KDA SUBUNIT | 3 | 91 | 8.3E-27 |
| 1 | g4118.t1 | Pfam | PF06645 | Microsomal signal peptidase 12 kDa subunit (SPC12) | 8 | 77 | 1.7E-27 |
| 7 | g4118.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 20 | - |
| 11 | g4118.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 39 | - |
| 9 | g4118.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 40 | 44 | - |
| 10 | g4118.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 66 | - |
| 8 | g4118.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 67 | 93 | - |
| 4 | g4118.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 19 | 38 | - |
| 5 | g4118.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 66 | - |
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 K12946 (signal peptidase complex subunit 1 [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.
