Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Signal peptidase complex subunit 2.

Parent gene

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.t5 TTS g8562.t5 31351893 31351893
chr_2 g8562 g8562.t5 isoform g8562.t5 31351930 31352697
chr_2 g8562 g8562.t5 exon g8562.t5.exon1 31351930 31352272
chr_2 g8562 g8562.t5 cds g8562.t5.CDS1 31351930 31352272
chr_2 g8562 g8562.t5 exon g8562.t5.exon2 31352334 31352697
chr_2 g8562 g8562.t5 cds g8562.t5.CDS2 31352334 31352461
chr_2 g8562 g8562.t5 TSS g8562.t5 31352783 31352783

Sequences

>g8562.t5 Gene=g8562 Length=707
ATGACACAAAAGAAAGCTGAAAAACAAGATGATAGTCAAGAGGTAAGTTGAATTTTATTT
ATGTGGCATTTAAAGCACTCGTAAATTGTTGAAAACTTGAAAATTTTATTATGGCCACAT
CATCATTCAAAAACAATTTAATTTCTAATATCATAAAATAACAGGTTGTTCAAATCAACA
AATGGGATGGAAGTCAAGTGAAGCATGCAATTGATGATGCATTCAAAACGGCTTTAATGG
AACGACCAAATTGTAAAGAACACTTTGCTATTATCGATGGACGACTCTTTATTTGCTTTC
TCGCTGTTGGAATTGCATTATTCGCATTAGGATATGATTATATTTACACATTCCCTACTT
CAAGGCCTGTTCTTATCATTTGTGTTACTTCATATTTCTTCCTTATGGGTGTTTTGACAA
TCTACACTACATACATTGAAAAGGGAATATTTGCTGTAGCAATTCAAAGTGATGGCAGTG
GAAAAACAATCAAAAAATGGACTGCAAGCTCAGAAATGAAGAAATATGATGACAAGTACA
CGTTAACATTAAGTGTAAAAGACTCAAAAAATGTTCGTGAGTTATCATCAACTAAATCAT
GTGCAAATTTTATTGATGTCGATGGTGTGGTTTGTAATGATTTAATCTCAGCTGAGCTCA
AAAGACTTTATAATTCATTAAATAATGCCGAAAAAAAAGATAAATAG

>g8562.t5 Gene=g8562 Length=156
MERPNCKEHFAIIDGRLFICFLAVGIALFALGYDYIYTFPTSRPVLIICVTSYFFLMGVL
TIYTTYIEKGIFAVAIQSDGSGKTIKKWTASSEMKKYDDKYTLTLSVKDSKNVRELSSTK
SCANFIDVDGVVCNDLISAELKRLYNSLNNAEKKDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g8562.t5 Coils Coil Coil 134 154 -
2 g8562.t5 PANTHER PTHR13085 MICROSOMAL SIGNAL PEPTIDASE 25 KDA SUBUNIT 7 154 4.1E-42
1 g8562.t5 Pfam PF06703 Microsomal signal peptidase 25 kDa subunit (SPC25) 5 145 3.4E-37
7 g8562.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
9 g8562.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 33 -
8 g8562.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 34 44 -
10 g8562.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 45 66 -
6 g8562.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 67 156 -
4 g8562.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 32 -
3 g8562.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 45 67 -

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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.

Raw TPM values