General information for g16954.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Presenilin-2.
Parent gene
- The parent gene g16954 is located on chr_4: 11861652..11862794 (+ 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_4 | g16954 | g16954.t1 | isoform | g16954.t1 | 11861652 | 11862794 |
| chr_4 | g16954 | g16954.t1 | exon | g16954.t1.exon1 | 11861652 | 11861957 |
| chr_4 | g16954 | g16954.t1 | cds | g16954.t1.CDS1 | 11861652 | 11861957 |
| chr_4 | g16954 | g16954.t1 | exon | g16954.t1.exon2 | 11862019 | 11862169 |
| chr_4 | g16954 | g16954.t1 | cds | g16954.t1.CDS2 | 11862019 | 11862169 |
| chr_4 | g16954 | g16954.t1 | exon | g16954.t1.exon3 | 11862284 | 11862323 |
| chr_4 | g16954 | g16954.t1 | cds | g16954.t1.CDS3 | 11862284 | 11862323 |
| chr_4 | g16954 | g16954.t1 | exon | g16954.t1.exon4 | 11862390 | 11862576 |
| chr_4 | g16954 | g16954.t1 | cds | g16954.t1.CDS4 | 11862390 | 11862576 |
| chr_4 | g16954 | g16954.t1 | exon | g16954.t1.exon5 | 11862639 | 11862794 |
| chr_4 | g16954 | g16954.t1 | cds | g16954.t1.CDS5 | 11862639 | 11862794 |
| chr_4 | g16954 | g16954.t1 | TTS | g16954.t1 | 11862911 | 11862911 |
| chr_4 | g16954 | g16954.t1 | TSS | g16954.t1 | NA | NA |
Sequences
>g16954.t1 Gene=g16954 Length=840
ATGACTGTGCTTTTGATTGTTCTATATAAAAAAAGATGCTACAGAATTATTCATGGCTGG
CTTATTATGTCAAGTTTCATGCTGTTGTTTTTATTTTCATATTTATATCTTGAAGAAGTT
TTAAGAGCATACAACATACCAATGGATTATCCAACAGCACTTTTTGTTATGTGGAACTTT
GGAGTTGTTGGAATGATTGCAATTCATTGGCAAGCACCATTGAGACTTCAACAAGCTTAT
TTGATTTTTGTCAGTGCATTAATGGCATTGGTTTTTGTCAAATATTTACCAGAATATACA
ACTTGGGTTGTTCTCGCTGTGATCTCAATTTGGGATTTAGTAGCAGTTTTATCACCAAAA
GGACCATTGAGAATTCTCGTTGAAACAGCTCAAGAAAGAAATGAACAAATTTTTCCAGCT
CTAATTTATTCATCAACTGTTTTATATTCAATTGTTGAATCAGCAGGATTTAATCAAGAA
TGGGCTTCAACAACAACAACTGTGACACGACCAGCAAGTGATAATTTGACAGAAGCTCAA
AGACAGCAACAACAAATGGAAGAAGAAGAGCGTGGAATTAAACTTGGTTTGGGTGATTTC
ATTTTTTATTCTGTGCTTGTTGGAAAAGCAAGCAGTTATGGTGACTGGAATACAACAATT
GCCTGCTTTGTTGCTATTTTGATTGGATTATGTTTGACACTTTTACTTTTGGCTGTAACA
CGTAAAGCACTTCCAGCATTGCCAATATCAATAACTTTTGGTCTTTTTTTCTGCTTTGCA
ACAAGTGTTATTGTGAAACCATTTACAGAAACTTTAGCAGCCGAACAAGTTTTCATCTAA
>g16954.t1 Gene=g16954 Length=279
MTVLLIVLYKKRCYRIIHGWLIMSSFMLLFLFSYLYLEEVLRAYNIPMDYPTALFVMWNF
GVVGMIAIHWQAPLRLQQAYLIFVSALMALVFVKYLPEYTTWVVLAVISIWDLVAVLSPK
GPLRILVETAQERNEQIFPALIYSSTVLYSIVESAGFNQEWASTTTTVTRPASDNLTEAQ
RQQQQMEEEERGIKLGLGDFIFYSVLVGKASSYGDWNTTIACFVAILIGLCLTLLLLAVT
RKALPALPISITFGLFFCFATSVIVKPFTETLAAEQVFI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g16954.t1 | Gene3D | G3DSA:1.10.472.100 | - | 166 | 271 | 9.8E-43 |
| 2 | g16954.t1 | PANTHER | PTHR10202:SF18 | PRESENILIN-1 | 1 | 166 | 7.8E-126 |
| 4 | g16954.t1 | PANTHER | PTHR10202 | PRESENILIN | 1 | 166 | 7.8E-126 |
| 3 | g16954.t1 | PANTHER | PTHR10202:SF18 | PRESENILIN-1 | 165 | 279 | 7.8E-126 |
| 5 | g16954.t1 | PANTHER | PTHR10202 | PRESENILIN | 165 | 279 | 7.8E-126 |
| 1 | g16954.t1 | Pfam | PF01080 | Presenilin | 1 | 176 | 2.5E-80 |
| 16 | g16954.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 19 | - |
| 26 | g16954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 37 | - |
| 21 | g16954.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 38 | 51 | - |
| 25 | g16954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 52 | 72 | - |
| 14 | g16954.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 73 | 78 | - |
| 23 | g16954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 79 | 96 | - |
| 20 | g16954.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 97 | 101 | - |
| 28 | g16954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 102 | 118 | - |
| 17 | g16954.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 119 | 191 | - |
| 22 | g16954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 192 | 210 | - |
| 19 | g16954.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 211 | 215 | - |
| 24 | g16954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 216 | 239 | - |
| 15 | g16954.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 240 | 245 | - |
| 27 | g16954.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 246 | 265 | - |
| 18 | g16954.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 266 | 279 | - |
| 12 | g16954.t1 | SMART | SM00730 | psh_8 | 1 | 265 | 3.4E-109 |
| 9 | g16954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
| 8 | g16954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 72 | - |
| 6 | g16954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 93 | - |
| 7 | g16954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 100 | 117 | - |
| 11 | g16954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 216 | 238 | - |
| 10 | g16954.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 243 | 265 | - |
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:0004190 | aspartic-type endopeptidase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04505 (presenilin 1 [EC:3.4.23.-])
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.
