Gene loci information

Transcript annotation

  • This transcript has been annotated as Lysosomal aspartic protease.

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 g17114 g17114.t4 isoform g17114.t4 12511177 12520362
chr_4 g17114 g17114.t4 exon g17114.t4.exon1 12511177 12511283
chr_4 g17114 g17114.t4 exon g17114.t4.exon2 12518068 12518297
chr_4 g17114 g17114.t4 cds g17114.t4.CDS1 12518210 12518297
chr_4 g17114 g17114.t4 exon g17114.t4.exon3 12518554 12518963
chr_4 g17114 g17114.t4 cds g17114.t4.CDS2 12518554 12518963
chr_4 g17114 g17114.t4 exon g17114.t4.exon4 12519024 12519251
chr_4 g17114 g17114.t4 cds g17114.t4.CDS3 12519024 12519251
chr_4 g17114 g17114.t4 exon g17114.t4.exon5 12519796 12519986
chr_4 g17114 g17114.t4 cds g17114.t4.CDS4 12519796 12519986
chr_4 g17114 g17114.t4 exon g17114.t4.exon6 12520047 12520222
chr_4 g17114 g17114.t4 cds g17114.t4.CDS5 12520047 12520222
chr_4 g17114 g17114.t4 exon g17114.t4.exon7 12520289 12520362
chr_4 g17114 g17114.t4 cds g17114.t4.CDS6 12520289 12520362
chr_4 g17114 g17114.t4 TSS g17114.t4 12520391 12520391
chr_4 g17114 g17114.t4 TTS g17114.t4 NA NA

Sequences

>g17114.t4 Gene=g17114 Length=1416
ATGTCAAAAAAGTTTAGTGCAACAATTTTTCTTCTCCTTCAGCTTTTGCTGATTGTAAAT
GGAAAACTATTGAGAATTCCTTTGTATAAATTTGAATCAGCAAGACGCCATTTTCAAACC
GTAGGAACAGATCTCACACAAGTTCGTCTTGCAAATGTTCAAGGACCAACACCAGAACCA
TTGTCAAATTATCTTGATGCCCAATATTATGGACCAATTACAATTGGAAGTCCACCACAA
AGTTTCAAAGTTGTTTTTGACACTGGAAGTTCAAATTTATGGGTTCCATCAAAATCTTGT
TCACTTATGAACATTGCCTGTCTTATGCATAACAAATATGATTCGAAAAAAAGTTCAACA
TACGAGAAAAATGGAACAAAATTTCATATCGAATACGGTAGCGGTTCACTAAGTGGCTTC
TTGTCAACTGATACTGTCGGTATTGGTGATTTAAAAATTCAAAAGCAAACATTTGCAGAA
GCAGTTTCAGAACCCGGTTTAGTTTTTGTTGCTGCTAAATTTGATGGAATTCTTGGATTA
GGCTACAAATCAATTTCAGTTGATGGAGTTGAACCAGTTTTCTATAACATGTACAATCAA
GGACTCATTTCAGAGCCAATTTTCTCATTTTATTTGAATCGTGATCCAAATGGCAAAGAA
GGTGGAGAAATTATTTTTGGTGGAAGTGATCCAGATCATTATGAAGGTGATTTCACTTAT
CTCCCAGTCAATCGCAAAGCATACTGGCAATTCAAAATGGATGGAGTGAAAATTGGTGAC
AAAACTTTCTGTAATGGTGGATGCCAAGCAATTGCTGACACTGGAACATCACTCATTGCT
GGACCAACTGATGAAGTTACAGCAATTAACAAAGCCATCGGTGGAACACCAATTTTAAAT
GGACAATACATGGTTAATTGTGACATGATACCAAATTTGCCTACAATTAAATTCACTTTG
GGTGGCAAGGAATTTGCACTTGATGGATCTGATTATATTTTAAGAATCGCTCAAATGGGT
AAAACTATTTGCTTGTCTGGTTTCATGGGAATTAATATTCCACCACCAAATGGACCACTA
TGGATTCTCGGTGATGTTTTTATTGGAAAATACTACACAGAATTTGATTTTGGCAATGAC
CGTGTTGGTTTTGCTGTCACAAAATAGACTCGACAAAAATTCCATTTTATTTTAGAGGCT
AAAAATCTCTCTCTATAAAAATATCAAAATATTTTTTTAATTTTGTGCCAGATGATCAAA
AAAAGAAATAAAAATTAATCTCAAAAAATAGAAATTTTATTTTAAATACAGAAATTTCTT
AGTTACTTTATGTAAACAACAGCAGCTGATAAAATATTTCATTATGAACATTTGAACTGT
AATAAAATAAAAAAAAACTTCATTTATCATTCACAC

>g17114.t4 Gene=g17114 Length=388
MSKKFSATIFLLLQLLLIVNGKLLRIPLYKFESARRHFQTVGTDLTQVRLANVQGPTPEP
LSNYLDAQYYGPITIGSPPQSFKVVFDTGSSNLWVPSKSCSLMNIACLMHNKYDSKKSST
YEKNGTKFHIEYGSGSLSGFLSTDTVGIGDLKIQKQTFAEAVSEPGLVFVAAKFDGILGL
GYKSISVDGVEPVFYNMYNQGLISEPIFSFYLNRDPNGKEGGEIIFGGSDPDHYEGDFTY
LPVNRKAYWQFKMDGVKIGDKTFCNGGCQAIADTGTSLIAGPTDEVTAINKAIGGTPILN
GQYMVNCDMIPNLPTIKFTLGGKEFALDGSDYILRIAQMGKTICLSGFMGINIPPPNGPL
WILGDVFIGKYYTEFDFGNDRVGFAVTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g17114.t4 Gene3D G3DSA:2.40.70.10 Acid Proteases 51 149 2.3E-41
11 g17114.t4 Gene3D G3DSA:2.40.70.10 Acid Proteases 150 387 2.6E-86
3 g17114.t4 PANTHER PTHR47966:SF42 CATHEPSIN D 15 386 3.3E-155
4 g17114.t4 PANTHER PTHR47966 BETA-SITE APP-CLEAVING ENZYME, ISOFORM A-RELATED 15 386 3.3E-155
8 g17114.t4 PRINTS PR00792 Pepsin (A1) aspartic protease family signature 75 95 8.7E-29
7 g17114.t4 PRINTS PR00792 Pepsin (A1) aspartic protease family signature 222 235 8.7E-29
6 g17114.t4 PRINTS PR00792 Pepsin (A1) aspartic protease family signature 270 281 8.7E-29
5 g17114.t4 PRINTS PR00792 Pepsin (A1) aspartic protease family signature 361 376 8.7E-29
1 g17114.t4 Pfam PF07966 A1 Propeptide 23 49 2.2E-4
2 g17114.t4 Pfam PF00026 Eukaryotic aspartyl protease 68 385 1.9E-128
14 g17114.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
15 g17114.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
16 g17114.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 17 -
17 g17114.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 21 -
13 g17114.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 388 -
19 g17114.t4 ProSitePatterns PS00141 Eukaryotic and viral aspartyl proteases active site. 84 95 -
20 g17114.t4 ProSitePatterns PS00141 Eukaryotic and viral aspartyl proteases active site. 270 281 -
21 g17114.t4 ProSiteProfiles PS51767 Peptidase family A1 domain profile. 69 385 82.796
9 g17114.t4 SUPERFAMILY SSF50630 Acid proteases 9 387 1.28E-129
10 g17114.t4 SignalP_EUK SignalP-TM SignalP-TM 1 21 -
18 g17114.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -

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:0006508 proteolysis BP
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