Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t5 TTS g1823.t5 13186290 13186290
chr_3 g1823 g1823.t5 isoform g1823.t5 13186521 13187154
chr_3 g1823 g1823.t5 exon g1823.t5.exon1 13186521 13186996
chr_3 g1823 g1823.t5 cds g1823.t5.CDS1 13186521 13186943
chr_3 g1823 g1823.t5 exon g1823.t5.exon2 13187086 13187154
chr_3 g1823 g1823.t5 TSS g1823.t5 13187240 13187240

Sequences

>g1823.t5 Gene=g1823 Length=545
ATGAGTTTACTCAAATCATTAGGAGCAGAGAGCCTGTTTGGCGATGTTTCGAGAATGGAT
AAAAGACAGTTTTGAGTTTTGGCATGATTGTATCGTCTGCTTTAATGATCTGGAAAGGAC
TAATGGTTGTGACAGGAAGTGAATCACCGATTGTTGTCGTATTAAGTGGATCCATGGAGC
CAGCATTTCATCGCGGTGATCTTCTCTTTCTCACAAATTATCCAGATGAGCCTGTGCGTG
TTGGAGAAATTGTAGTTTTTAAAGTCGAGGGTCGAGATATACCTATTGTGCACAGAGTTA
TCAAACTACATGAAAAATCGGACGGTTCAGTGAAATTTTTGACTAAAGGTGATAACAATT
CAGTCGATGATAGAGGTCTTTATGCTCCAGGACAACTTTGGCTTACGAAAAAAGATATTG
TAGGAAGAGCGCGAGGTTTTTTACCTTATGTTGGAATGATTACTATCCTGATGAATGAGT
ACCCCAACTTTAAATTTGCTATTTTAGGTATTTTAGCAATTTATGTTCTATTGCACCGAG
AATAA

>g1823.t5 Gene=g1823 Length=140
MVVTGSESPIVVVLSGSMEPAFHRGDLLFLTNYPDEPVRVGEIVVFKVEGRDIPIVHRVI
KLHEKSDGSVKFLTKGDNNSVDDRGLYAPGQLWLTKKDIVGRARGFLPYVGMITILMNEY
PNFKFAILGILAIYVLLHRE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1823.t5 CDD cd06530 S26_SPase_I 9 103 1.70402E-21
8 g1823.t5 Coils Coil Coil 134 140 -
7 g1823.t5 Gene3D G3DSA:2.10.109.10 Umud Fragment 9 114 1.7E-6
2 g1823.t5 PANTHER PTHR10806:SF12 SIGNAL PEPTIDASE COMPLEX CATALYTIC SUBUNIT SEC11C 1 140 2.4E-74
3 g1823.t5 PANTHER PTHR10806 SIGNAL PEPTIDASE COMPLEX CATALYTIC SUBUNIT SEC11 1 140 2.4E-74
5 g1823.t5 PRINTS PR00728 Eukaryotic signal peptidase (S26B) family signature 13 28 2.8E-12
4 g1823.t5 PRINTS PR00728 Eukaryotic signal peptidase (S26B) family signature 72 83 2.8E-12
1 g1823.t5 Pfam PF00717 Peptidase S24-like 4 88 3.8E-8
10 g1823.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 119 -
11 g1823.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 120 137 -
9 g1823.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 138 140 -
15 g1823.t5 ProSitePatterns PS00501 Signal peptidases I serine active site. 15 22 -
14 g1823.t5 ProSitePatterns PS00761 Signal peptidases I signature 3. 72 85 -
6 g1823.t5 SUPERFAMILY SSF51306 LexA/Signal peptidase 10 113 1.22E-11
16 g1823.t5 TIGRFAM TIGR02228 sigpep_I_arch: signal peptidase I 5 135 6.0E-29
13 g1823.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 137 -

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.

Raw TPM values