Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Signal peptidase complex catalytic subunit SEC11C.

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_3 g1823 g1823.t4 TTS g1823.t4 13186290 13186290
chr_3 g1823 g1823.t4 isoform g1823.t4 13186521 13187154
chr_3 g1823 g1823.t4 exon g1823.t4.exon1 13186521 13186602
chr_3 g1823 g1823.t4 cds g1823.t4.CDS1 13186588 13186602
chr_3 g1823 g1823.t4 exon g1823.t4.exon2 13186779 13187009
chr_3 g1823 g1823.t4 cds g1823.t4.CDS2 13186779 13187009
chr_3 g1823 g1823.t4 exon g1823.t4.exon3 13187086 13187154
chr_3 g1823 g1823.t4 cds g1823.t4.CDS3 13187086 13187154
chr_3 g1823 g1823.t4 TSS g1823.t4 13187240 13187240

Sequences

>g1823.t4 Gene=g1823 Length=382
ATGAGTTTACTCAAATCATTAGGAGCAGAGAGCCTGTTTGGCGATGTTTCGAGAATGGAT
AAAAGACAGTTTTTCTATCAAGTTTTGAGTTTTGGCATGATTGTATCGTCTGCTTTAATG
ATCTGGAAAGGACTAATGGTTGTGACAGGAAGTGAATCACCGATTGTTGTCGTATTAAGT
GGATCCATGGAGCCAGCATTTCATCGCGGTGATCTTCTCTTTCTCACAAATTATCCAGAT
GAGCCTGTGCGTGTTGGAGAAATTGTAGTTTTTAAAGTCGAGGGTCGAGATATACCTATT
TATCCTGATGAATGAGTACCCCAACTTTAAATTTGCTATTTTAGGTATTTTAGCAATTTA
TGTTCTATTGCACCGAGAATAA

>g1823.t4 Gene=g1823 Length=104
MSLLKSLGAESLFGDVSRMDKRQFFYQVLSFGMIVSSALMIWKGLMVVTGSESPIVVVLS
GSMEPAFHRGDLLFLTNYPDEPVRVGEIVVFKVEGRDIPIYPDE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g1823.t4 CDD cd06530 S26_SPase_I 54 97 1.1161E-10
2 g1823.t4 PANTHER PTHR10806:SF28 SIGNAL PEPTIDASE COMPLEX CATALYTIC SUBUNIT SEC11A 12 100 1.2E-46
3 g1823.t4 PANTHER PTHR10806 SIGNAL PEPTIDASE COMPLEX CATALYTIC SUBUNIT SEC11 12 100 1.2E-46
1 g1823.t4 Pfam PF00717 Peptidase S24-like 41 95 1.9E-6
6 g1823.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 23 -
7 g1823.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 24 42 -
5 g1823.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 43 104 -
10 g1823.t4 ProSitePatterns PS00501 Signal peptidases I serine active site. 60 67 -
4 g1823.t4 SUPERFAMILY SSF51306 LexA/Signal peptidase 55 94 1.44E-7
11 g1823.t4 TIGRFAM TIGR02228 sigpep_I_arch: signal peptidase I 27 100 5.5E-16
9 g1823.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 28 50 -

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:0016020 membrane CC
GO:0004252 serine-type endopeptidase activity MF
GO:0008233 peptidase activity MF
GO:0016021 integral component of membrane CC
GO:0008236 serine-type peptidase activity MF
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. There were no conditions that were differentially expressed