General information for g8562.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Signal peptidase complex subunit 2.
Parent gene
- The parent gene g8562 is located on chr_2: 31351930..31352697 (- 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 | g8562 | g8562.t3 | isoform | g8562.t3 | 31348423 | 31352697 |
| chr_2 | g8562 | g8562.t3 | exon | g8562.t3.exon1 | 31348423 | 31348695 |
| chr_2 | g8562 | g8562.t3 | exon | g8562.t3.exon2 | 31351719 | 31352272 |
| chr_2 | g8562 | g8562.t3 | cds | g8562.t3.CDS1 | 31351930 | 31352272 |
| chr_2 | g8562 | g8562.t3 | exon | g8562.t3.exon3 | 31352334 | 31352533 |
| chr_2 | g8562 | g8562.t3 | cds | g8562.t3.CDS2 | 31352334 | 31352533 |
| chr_2 | g8562 | g8562.t3 | exon | g8562.t3.exon4 | 31352656 | 31352697 |
| chr_2 | g8562 | g8562.t3 | cds | g8562.t3.CDS3 | 31352656 | 31352697 |
| chr_2 | g8562 | g8562.t3 | TSS | g8562.t3 | 31352783 | 31352783 |
| chr_2 | g8562 | g8562.t3 | TTS | g8562.t3 | NA | NA |
Sequences
>g8562.t3 Gene=g8562 Length=1069
ATGACACAAAAGAAAGCTGAAAAACAAGATGATAGTCAAGAGGTTGTTCAAATCAACAAA
TGGGATGGAAGTCAAGTGAAGCATGCAATTGATGATGCATTCAAAACGGCTTTAATGGAA
CGACCAAATTGTAAAGAACACTTTGCTATTATCGATGGACGACTCTTTATTTGCTTTCTC
GCTGTTGGAATTGCATTATTCGCATTAGGATATGATTATATTTACACATTCCCTACTTCA
AGGCCTGTTCTTATCATTTGTGTTACTTCATATTTCTTCCTTATGGGTGTTTTGACAATC
TACACTACATACATTGAAAAGGGAATATTTGCTGTAGCAATTCAAAGTGATGGCAGTGGA
AAAACAATCAAAAAATGGACTGCAAGCTCAGAAATGAAGAAATATGATGACAAGTACACG
TTAACATTAAGTGTAAAAGACTCAAAAAATGTTCGTGAGTTATCATCAACTAAATCATGT
GCAAATTTTATTGATGTCGATGGTGTGGTTTGTAATGATTTAATCTCAGCTGAGCTCAAA
AGACTTTATAATTCATTAAATAATGCCGAAAAAAAAGATAAATAGTTCGAACAAGTCTAA
ATAAAAACTTTCTCATCTCCCTAAATTTCAATGATTTTCGATTTCATTTTTATGATTTGA
GTAAAATTTCATGTCTAATTTTTATTAAATATTTTATTAAATGTGAATATATACACAAAA
GATTCTTAAAAATAAAATAAAGCAAAAAATAAATTACAAGTTACACCGTCTTAGCCAAAC
AGGTCTATTTAAAATTAAGTGTTCCTGAAATATGTTTCGCGTACACGCAGTCGTTCTTCT
TAAAAAATAGATTCCAACCAGTTTAAAATAAATTATGTAACAACAATGTGATGTTGGTCA
TTTCCTCTTTTATACAATGTGTTCGATTTTCTTTTCATGACCACCGATGACATTCATTCA
ATTAAATCATAGAAAAAAAATAATTGTGCATTCCTCATACACATTGACTATTCAAGCAAG
TGGCATATATGCACATTTTTTATCGCATTATCTTAAATTCATTACAAAA
>g8562.t3 Gene=g8562 Length=194
MTQKKAEKQDDSQEVVQINKWDGSQVKHAIDDAFKTALMERPNCKEHFAIIDGRLFICFL
AVGIALFALGYDYIYTFPTSRPVLIICVTSYFFLMGVLTIYTTYIEKGIFAVAIQSDGSG
KTIKKWTASSEMKKYDDKYTLTLSVKDSKNVRELSSTKSCANFIDVDGVVCNDLISAELK
RLYNSLNNAEKKDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g8562.t3 | Coils | Coil | Coil | 172 | 194 | - |
| 2 | g8562.t3 | PANTHER | PTHR13085 | MICROSOMAL SIGNAL PEPTIDASE 25 KDA SUBUNIT | 1 | 192 | 2.2E-54 |
| 1 | g8562.t3 | Pfam | PF06703 | Microsomal signal peptidase 25 kDa subunit (SPC25) | 26 | 183 | 1.6E-41 |
| 6 | g8562.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 47 | - |
| 10 | g8562.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 48 | 71 | - |
| 8 | g8562.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 72 | 82 | - |
| 9 | g8562.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 83 | 104 | - |
| 7 | g8562.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 105 | 194 | - |
| 3 | g8562.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 77 | - |
| 4 | g8562.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 104 | - |
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 K12947 (signal peptidase complex subunit 2 [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.
