Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Gamma-secretase subunit Aph-1.

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_1 g14009 g14009.t2 isoform g14009.t2 33975170 33975960
chr_1 g14009 g14009.t2 exon g14009.t2.exon1 33975170 33975960
chr_1 g14009 g14009.t2 cds g14009.t2.CDS1 33975473 33975778
chr_1 g14009 g14009.t2 TSS g14009.t2 33976352 33976352
chr_1 g14009 g14009.t2 TTS g14009.t2 NA NA

Sequences

>g14009.t2 Gene=g14009 Length=791
TCCGTTTTATAGTTTATAAATTATTGGATAAAACTAGTGCAGGTTTAGAAGAGTTGGCCG
GAAATTCATTAGTAATTCATAATAAAACAGTGCTCGCATATGTGTCTGGTCTCGGTTTTG
GCATCATTTCAGGCTTATTTCAAAGTGTTAATATACTCGCTGATGCTTTAGGTCCAGGAA
CAATGGGTTTAAAAAGTGGCTCAGAAATGTTCTTCCTTACAAGTGCTACAATGGCATTGT
GCATAATTCTTTTACATACATTTTGGAGCATTATTTTTTTTGATGGCATTCATCATCGAA
ACAAAGCTCATCTCTCTTTTGTCATATTAAGTCATTTATTTTTTTCAATAACGACTCTAC
TTAACTCAAGCGAAATTTATAGTTTAACAATTATTTTGAGTGTGATCAATGTGATTTTGA
CAATGTGCTTTGCATTTAAAATCGTAGGTGGTACTTTTGAAAAATTAAAGAGATGTATCA
TTTGTTAATAATTTAATATCACATTTAATTTGTAACAATAATACTATCTGATATCATTAT
TAAAGAAAGCTCTTAATTATCGCTGTAATCATTTTAATAATCCATTTTTATAAGAAAAAG
ACTTGAATTATAAGATGCTAATAAAAGATGACGAAAACATTTTTAATTTATTATTGTATT
AAGATAACAAATTTAAGAAAGATGATTTGAAAGAATTTACGAGCAAGATATTTGTAATCA
TAACGGAGAAATAAATCATTTTTTGAATTTTTTTAAAAAGTTGCTAAGCGTATTCCCCCT
AAAATTGTTCA

>g14009.t2 Gene=g14009 Length=101
MGLKSGSEMFFLTSATMALCIILLHTFWSIIFFDGIHHRNKAHLSFVILSHLFFSITTLL
NSSEIYSLTIILSVINVILTMCFAFKIVGGTFEKLKRCIIC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g14009.t2 PANTHER PTHR12889 GAMMA-SECRETASE SUBUNIT APH-1 2 101 4.7E-18
1 g14009.t2 Pfam PF06105 Aph-1 protein 1 94 9.0E-24
8 g14009.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
10 g14009.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 33 -
7 g14009.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 34 41 -
12 g14009.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 42 60 -
9 g14009.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 61 65 -
11 g14009.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -
6 g14009.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 89 101 -
5 g14009.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 32 -
4 g14009.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 66 -
3 g14009.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 70 92 -

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:0016485 protein processing BP
GO:0016021 integral component of membrane CC
GO:0043085 positive regulation of catalytic activity BP

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