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.t2 TTS g1823.t2 13186290 13186290
chr_3 g1823 g1823.t2 isoform g1823.t2 13186291 13187007
chr_3 g1823 g1823.t2 exon g1823.t2.exon1 13186291 13187007
chr_3 g1823 g1823.t2 cds g1823.t2.CDS1 13186521 13186982
chr_3 g1823 g1823.t2 TSS g1823.t2 13187240 13187240

Sequences

>g1823.t2 Gene=g1823 Length=717
TTTCTATCAAGTTTTGAGTTTTGGCATGATTGTATCGTCTGCTTTAATGATCTGGAAAGG
ACTAATGGTTGTGACAGGAAGTGAATCACCGATTGTTGTCGTATTAAGTGGATCCATGGA
GCCAGCATTTCATCGCGGTGATCTTCTCTTTCTCACAAATTATCCAGATGAGCCTGTGCG
TGTTGGAGAAATTGTAGTTTTTAAAGTCGAGGGTCGAGATATACCTATTGTGCACAGAGT
TATCAAACTACATGAAAAATCGGACGGTTCAGTGAAATTTTTGACTAAAGGTGATAACAA
TTCAGTCGATGATAGAGGTCTTTATGCTCCAGGACAACTTTGGCTTACGAAAAAAGATAT
TGTAGGAAGAGCGCGAGGTTTTTTACCTTATGTTGGAATGATTACTATCCTGATGAATGA
GTACCCCAACTTTAAATTTGCTATTTTAGGTATTTTAGCAATTTATGTTCTATTGCACCG
AGAATAATCTAAAATACTTACATTCTCTTTAAATCGCTGAAAAGAGTAAATAATTTATAA
GACAACTCTTTTTTCGAACTATACTATGCGTTATTCAAATTTTATGCACACGAAAATTTA
TGTTAAGTCAAATTTTTCTCAAAAATATAACTTCCATGCCAGCGAACAGTACATTTAAAA
AAATTTTGTGAATGAAAACTGAAGAAAAATAACATATGATTTAAATTTTTGATAAGT

>g1823.t2 Gene=g1823 Length=153
MIVSSALMIWKGLMVVTGSESPIVVVLSGSMEPAFHRGDLLFLTNYPDEPVRVGEIVVFK
VEGRDIPIVHRVIKLHEKSDGSVKFLTKGDNNSVDDRGLYAPGQLWLTKKDIVGRARGFL
PYVGMITILMNEYPNFKFAILGILAIYVLLHRE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g1823.t2 CDD cd06530 S26_SPase_I 22 116 1.43954E-21
8 g1823.t2 Gene3D G3DSA:2.10.109.10 Umud Fragment 22 126 2.3E-6
2 g1823.t2 PANTHER PTHR10806:SF12 SIGNAL PEPTIDASE COMPLEX CATALYTIC SUBUNIT SEC11C 1 153 1.1E-82
3 g1823.t2 PANTHER PTHR10806 SIGNAL PEPTIDASE COMPLEX CATALYTIC SUBUNIT SEC11 1 153 1.1E-82
5 g1823.t2 PRINTS PR00728 Eukaryotic signal peptidase (S26B) family signature 26 41 3.1E-12
4 g1823.t2 PRINTS PR00728 Eukaryotic signal peptidase (S26B) family signature 85 96 3.1E-12
1 g1823.t2 Pfam PF00717 Peptidase S24-like 10 101 1.1E-8
10 g1823.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 132 -
11 g1823.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 133 150 -
9 g1823.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 151 153 -
15 g1823.t2 ProSitePatterns PS00501 Signal peptidases I serine active site. 28 35 -
14 g1823.t2 ProSitePatterns PS00761 Signal peptidases I signature 3. 85 98 -
6 g1823.t2 SUPERFAMILY SSF51306 LexA/Signal peptidase 23 124 1.23E-11
7 g1823.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 18 -
16 g1823.t2 TIGRFAM TIGR02228 sigpep_I_arch: signal peptidase I 7 148 3.3E-30
13 g1823.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 128 150 -

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

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.

Raw TPM values