Gene loci information

Transcript annotation

  • This transcript has been annotated as Presenilin-like protein.

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_4 g16954 g16954.t2 isoform g16954.t2 11861652 11862794
chr_4 g16954 g16954.t2 exon g16954.t2.exon1 11861652 11861957
chr_4 g16954 g16954.t2 cds g16954.t2.CDS1 11861652 11861957
chr_4 g16954 g16954.t2 exon g16954.t2.exon2 11862019 11862230
chr_4 g16954 g16954.t2 cds g16954.t2.CDS2 11862019 11862228
chr_4 g16954 g16954.t2 exon g16954.t2.exon3 11862284 11862576
chr_4 g16954 g16954.t2 exon g16954.t2.exon4 11862639 11862794
chr_4 g16954 g16954.t2 TTS g16954.t2 11862911 11862911
chr_4 g16954 g16954.t2 TSS g16954.t2 NA NA

Sequences

>g16954.t2 Gene=g16954 Length=967
ATGACTGTGCTTTTGATTGTTCTATATAAAAAAAGATGCTACAGAATTATTCATGGCTGG
CTTATTATGTCAAGTTTCATGCTGTTGTTTTTATTTTCATATTTATATCTTGAAGAAGTT
TTAAGAGCATACAACATACCAATGGATTATCCAACAGCACTTTTTGTTATGTGGAACTTT
GGAGTTGTTGGAATGATTGCAATTCATTGGCAAGCACCATTGAGACTTCAACAAGCTTAT
TTGATTTTTGTCAGTGCATTAATGGCATTGGTTTTTGTCAAATATTTACCAGAATATACA
ACTTGGGTTGTTCTCGCTGTGATCTCAATTTGGGATTTAGTAGCAGTTTTATCACCAAAA
GGACCATTGAGAATTCTCGTTGAAACAGCTCAAGAAAGAAATGAACAAATTTTTCCAGCT
CTAATTTATTCATCAACTGTTTTATATTCAATTGTTGGTACAACAACAACTGATGATGAT
GACCAACAAAGAAATGAATCAAAGAAGACAAAATGATGAATCAGCAGGATTTAATCAAGA
ATGGGCTTCAACAACAACGTCAAAGAATTCAACAACGGCAAGTTGAAGTTCAAGCAAATG
ATCAAAATGACCAACTCAATATAGAACTGTGACACGACCAGCAAGTGATAATTTGACAGA
AGCTCAAAGACAGCAACAACAAATGGAAGAAGAAGAGCGTGGAATTAAACTTGGTTTGGG
TGATTTCATTTTTTATTCTGTGCTTGTTGGAAAAGCAAGCAGTTATGGTGACTGGAATAC
AACAATTGCCTGCTTTGTTGCTATTTTGATTGGATTATGTTTGACACTTTTACTTTTGGC
TGTAACACGTAAAGCACTTCCAGCATTGCCAATATCAATAACTTTTGGTCTTTTTTTCTG
CTTTGCAACAAGTGTTATTGTGAAACCATTTACAGAAACTTTAGCAGCCGAACAAGTTTT
CATCTAA

>g16954.t2 Gene=g16954 Length=171
MTVLLIVLYKKRCYRIIHGWLIMSSFMLLFLFSYLYLEEVLRAYNIPMDYPTALFVMWNF
GVVGMIAIHWQAPLRLQQAYLIFVSALMALVFVKYLPEYTTWVVLAVISIWDLVAVLSPK
GPLRILVETAQERNEQIFPALIYSSTVLYSIVGTTTTDDDDQQRNESKKTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g16954.t2 PANTHER PTHR10202 PRESENILIN 1 168 1.7E-84
3 g16954.t2 PANTHER PTHR10202:SF24 PRESENILIN-2 1 168 1.7E-84
1 g16954.t2 Pfam PF01080 Presenilin 1 168 3.5E-82
10 g16954.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
16 g16954.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 37 -
13 g16954.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 38 51 -
15 g16954.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 72 -
9 g16954.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 73 78 -
14 g16954.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 79 96 -
12 g16954.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 97 101 -
17 g16954.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 102 118 -
11 g16954.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 119 171 -
8 g16954.t2 SMART SM00730 psh_8 1 171 3.3E-32
7 g16954.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
6 g16954.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 72 -
4 g16954.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 79 96 -
5 g16954.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 100 117 -

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

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