Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t3 TTS g14009.t3 33975322 33975322
chr_1 g14009 g14009.t3 isoform g14009.t3 33975473 33976349
chr_1 g14009 g14009.t3 exon g14009.t3.exon1 33975473 33975967
chr_1 g14009 g14009.t3 cds g14009.t3.CDS1 33975473 33975967
chr_1 g14009 g14009.t3 exon g14009.t3.exon2 33976042 33976270
chr_1 g14009 g14009.t3 cds g14009.t3.CDS2 33976042 33976270
chr_1 g14009 g14009.t3 exon g14009.t3.exon3 33976332 33976349
chr_1 g14009 g14009.t3 cds g14009.t3.CDS3 33976332 33976339
chr_1 g14009 g14009.t3 TSS g14009.t3 33976352 33976352

Sequences

>g14009.t3 Gene=g14009 Length=742
TTCGCAAAAGATGCAAAACAATAAAATGACTTTAGCCGAGTTTTTTGGATGCGCTTTTCT
CGCTTTTGGGCCGCCATTGGCAATGTTCTGTTACACAATCAGTGATTCTCCGATAAAGAT
AATTTTATTAATATTTTCTTCATTCCTGTGGCTTCTTGCTTTATTGTTATCATCAATAAT
TTGGTTTATATTCATTCCATTAAAAAGTTATCTCATCTTTGGAGTAGTTGTATCTGTGCT
GATTCAGGAAGCTTTCCGTTTTATAGTTTATAAATTATTGGATAAAACTAGTGCAGGTTT
AGAAGAGTTGGCCGGAAATTCATTAGTAATTCATAATAAAACAGTGCTCGCATATGTGTC
TGGTCTCGGTTTTGGCATCATTTCAGGCTTATTTCAAAGTGTTAATATACTCGCTGATGC
TTTAGGTCCAGGAACAATGGGTTTAAAAAGTGGCTCAGAAATGTTCTTCCTTACAAGTGC
TACAATGGCATTGTGCATAATTCTTTTACATACATTTTGGAGCATTATTTTTTTTGATGG
CATTCATCATCGAAACAAAGCTCATCTCTCTTTTGTCATATTAAGTCATTTATTTTTTTC
AATAACGACTCTACTTAACTCAAGCGAAATTTATAGTTTAACAATTATTTTGAGTGTGAT
CAATGTGATTTTGACAATGTGCTTTGCATTTAAAATCGTAGGTGGTACTTTTGAAAAATT
AAAGAGATGTATCATTTGTTAA

>g14009.t3 Gene=g14009 Length=243
MQNNKMTLAEFFGCAFLAFGPPLAMFCYTISDSPIKIILLIFSSFLWLLALLLSSIIWFI
FIPLKSYLIFGVVVSVLIQEAFRFIVYKLLDKTSAGLEELAGNSLVIHNKTVLAYVSGLG
FGIISGLFQSVNILADALGPGTMGLKSGSEMFFLTSATMALCIILLHTFWSIIFFDGIHH
RNKAHLSFVILSHLFFSITTLLNSSEIYSLTIILSVINVILTMCFAFKIVGGTFEKLKRC
IIC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g14009.t3 PANTHER PTHR12889 GAMMA-SECRETASE SUBUNIT APH-1 6 243 6.3E-74
1 g14009.t3 Pfam PF06105 Aph-1 protein 7 236 1.8E-84
16 g14009.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
24 g14009.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 30 -
13 g14009.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 31 36 -
23 g14009.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 61 -
15 g14009.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 62 66 -
19 g14009.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 67 90 -
10 g14009.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 91 110 -
20 g14009.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 111 131 -
14 g14009.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 132 150 -
21 g14009.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 151 172 -
11 g14009.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 173 183 -
22 g14009.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 184 202 -
17 g14009.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 203 207 -
18 g14009.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 208 230 -
12 g14009.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 231 243 -
4 g14009.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 6 28 -
3 g14009.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 40 62 -
8 g14009.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
7 g14009.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 112 131 -
6 g14009.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 151 173 -
5 g14009.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 185 202 -
9 g14009.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 212 234 -

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

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