General information for g4809.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g4809 is located on chr_2: 5065988..5066362 (- 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_2 | g4809 | g4809.t1 | TTS | g4809.t1 | 5065894 | 5065894 |
| chr_2 | g4809 | g4809.t1 | isoform | g4809.t1 | 5065988 | 5066362 |
| chr_2 | g4809 | g4809.t1 | exon | g4809.t1.exon1 | 5065988 | 5066127 |
| chr_2 | g4809 | g4809.t1 | cds | g4809.t1.CDS1 | 5065988 | 5066127 |
| chr_2 | g4809 | g4809.t1 | exon | g4809.t1.exon2 | 5066184 | 5066287 |
| chr_2 | g4809 | g4809.t1 | cds | g4809.t1.CDS2 | 5066184 | 5066287 |
| chr_2 | g4809 | g4809.t1 | exon | g4809.t1.exon3 | 5066349 | 5066362 |
| chr_2 | g4809 | g4809.t1 | cds | g4809.t1.CDS3 | 5066349 | 5066362 |
| chr_2 | g4809 | g4809.t1 | TSS | g4809.t1 | 5066481 | 5066481 |
Sequences
>g4809.t1 Gene=g4809 Length=258
ATGGTATTTTCGAGCGGGATTTCTTTTTCTTCTTTTGTATGGCTGATAAATTTCTTTTGG
TTTTATGATTCTGCATTCAAACAACCACCTTTTGATGAACAGAATACTATAAGAAAATAT
GTGATAATGTCTGGAATCGGAACATTATTTTGGATAATTGCTCTTACAACATGGATTATC
ATATTTCAAACAAACCGTATTGCTTGGGGAGAATTTGGTGACGAATTAAGTTTTATTATT
CCATTAGGATCAAAATAA
>g4809.t1 Gene=g4809 Length=85
MVFSSGISFSSFVWLINFFWFYDSAFKQPPFDEQNTIRKYVIMSGIGTLFWIIALTTWII
IFQTNRIAWGEFGDELSFIIPLGSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 1 | g4809.t1 | Pfam | PF10251 | Presenilin enhancer-2 subunit of gamma secretase | 2 | 83 | 5.1E-29 |
| 6 | g4809.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 8 | g4809.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 22 | - |
| 4 | g4809.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 23 | 41 | - |
| 7 | g4809.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 42 | 61 | - |
| 5 | g4809.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 62 | 85 | - |
| 3 | g4809.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 2 | 20 | - |
| 2 | g4809.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 40 | 62 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K06170 (presenilin enhancer 2)
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.
