General information for g14009.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Gamma-secretase subunit Aph-1.
Parent gene
- The parent gene g14009 is located on chr_1: 33975473..33976349 (- strand)
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.t1 | TTS | g14009.t1 | 33975322 | 33975322 |
| chr_1 | g14009 | g14009.t1 | isoform | g14009.t1 | 33975473 | 33976263 |
| chr_1 | g14009 | g14009.t1 | exon | g14009.t1.exon1 | 33975473 | 33975967 |
| chr_1 | g14009 | g14009.t1 | cds | g14009.t1.CDS1 | 33975473 | 33975967 |
| chr_1 | g14009 | g14009.t1 | exon | g14009.t1.exon2 | 33976042 | 33976263 |
| chr_1 | g14009 | g14009.t1 | cds | g14009.t1.CDS2 | 33976042 | 33976263 |
| chr_1 | g14009 | g14009.t1 | TSS | g14009.t1 | 33976352 | 33976352 |
Sequences
>g14009.t1 Gene=g14009 Length=717
ATGACTTTAGCCGAGTTTTTTGGATGCGCTTTTCTCGCTTTTGGGCCGCCATTGGCAATG
TTCTGTTACACAATCAGTGATTCTCCGATAAAGATAATTTTATTAATATTTTCTTCATTC
CTGTGGCTTCTTGCTTTATTGTTATCATCAATAATTTGGTTTATATTCATTCCATTAAAA
AGTTATCTCATCTTTGGAGTAGTTGTATCTGTGCTGATTCAGGAAGCTTTCCGTTTTATA
GTTTATAAATTATTGGATAAAACTAGTGCAGGTTTAGAAGAGTTGGCCGGAAATTCATTA
GTAATTCATAATAAAACAGTGCTCGCATATGTGTCTGGTCTCGGTTTTGGCATCATTTCA
GGCTTATTTCAAAGTGTTAATATACTCGCTGATGCTTTAGGTCCAGGAACAATGGGTTTA
AAAAGTGGCTCAGAAATGTTCTTCCTTACAAGTGCTACAATGGCATTGTGCATAATTCTT
TTACATACATTTTGGAGCATTATTTTTTTTGATGGCATTCATCATCGAAACAAAGCTCAT
CTCTCTTTTGTCATATTAAGTCATTTATTTTTTTCAATAACGACTCTACTTAACTCAAGC
GAAATTTATAGTTTAACAATTATTTTGAGTGTGATCAATGTGATTTTGACAATGTGCTTT
GCATTTAAAATCGTAGGTGGTACTTTTGAAAAATTAAAGAGATGTATCATTTGTTAA
>g14009.t1 Gene=g14009 Length=238
MTLAEFFGCAFLAFGPPLAMFCYTISDSPIKIILLIFSSFLWLLALLLSSIIWFIFIPLK
SYLIFGVVVSVLIQEAFRFIVYKLLDKTSAGLEELAGNSLVIHNKTVLAYVSGLGFGIIS
GLFQSVNILADALGPGTMGLKSGSEMFFLTSATMALCIILLHTFWSIIFFDGIHHRNKAH
LSFVILSHLFFSITTLLNSSEIYSLTIILSVINVILTMCFAFKIVGGTFEKLKRCIIC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g14009.t1 | PANTHER | PTHR12889 | GAMMA-SECRETASE SUBUNIT APH-1 | 1 | 238 | 5.8E-74 |
| 1 | g14009.t1 | Pfam | PF06105 | Aph-1 protein | 2 | 231 | 1.6E-84 |
| 16 | g14009.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 20 | g14009.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 10 | g14009.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 26 | 31 | - |
| 19 | g14009.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 32 | 56 | - |
| 17 | g14009.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 57 | 61 | - |
| 18 | g14009.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 62 | 85 | - |
| 12 | g14009.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 86 | 105 | - |
| 22 | g14009.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 106 | 126 | - |
| 15 | g14009.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 127 | 145 | - |
| 21 | g14009.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 167 | - |
| 13 | g14009.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 168 | 178 | - |
| 23 | g14009.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 179 | 197 | - |
| 14 | g14009.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 198 | 202 | - |
| 24 | g14009.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 225 | - |
| 11 | g14009.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 226 | 238 | - |
| 3 | g14009.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 4 | 26 | - |
| 9 | g14009.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 57 | - |
| 8 | g14009.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 62 | 81 | - |
| 6 | g14009.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 107 | 126 | - |
| 7 | g14009.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 168 | - |
| 4 | g14009.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 180 | 197 | - |
| 5 | g14009.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 207 | 229 | - |
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 transcript has been annotated with K06172 (gamma-secretase subunit APH-1)
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.
