Gene loci information

Transcript annotation

  • This transcript has been annotated as Trypsin-3.

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_2 g4558 g4558.t4 TSS g4558.t4 3235559 3235559
chr_2 g4558 g4558.t4 isoform g4558.t4 3235587 3236652
chr_2 g4558 g4558.t4 exon g4558.t4.exon1 3235587 3235800
chr_2 g4558 g4558.t4 cds g4558.t4.CDS1 3235587 3235800
chr_2 g4558 g4558.t4 exon g4558.t4.exon2 3235915 3236279
chr_2 g4558 g4558.t4 cds g4558.t4.CDS2 3235915 3236279
chr_2 g4558 g4558.t4 exon g4558.t4.exon3 3236338 3236377
chr_2 g4558 g4558.t4 cds g4558.t4.CDS3 3236338 3236377
chr_2 g4558 g4558.t4 exon g4558.t4.exon4 3236438 3236533
chr_2 g4558 g4558.t4 cds g4558.t4.CDS4 3236438 3236533
chr_2 g4558 g4558.t4 exon g4558.t4.exon5 3236594 3236652
chr_2 g4558 g4558.t4 cds g4558.t4.CDS5 3236594 3236652
chr_2 g4558 g4558.t4 TTS g4558.t4 3236809 3236809

Sequences

>g4558.t4 Gene=g4558 Length=774
ATGAGATCGCTTTGGTTGATCTTGATTTTTGTACTTTCTGCGTTGATCTCAAAATGTAAT
AGTAGAGAAGCAAGAGCAATTAGTGGTAGAATTGTTGGAGGTGTTGAAGTCGATATTGAA
AAAATTCCTTATCAAGTTTCTTTACTATATTACGATTCTTTAGCATGTGGTGCAAGCATT
TTAAGTTGCAAATTTGTTTTAACAGCTGCTCATTATTTATTAAAAATTTGTTTAATTATA
GTTCGTGCAGGATCTTCCACTTTTTTTGAGGGTGGTTCTATACATGATGTCAGTAAAATT
GATATCCATCCACAATATAATAGAACACTTTTAGATTATGATGCTGCAATTTTGACTTTA
AGAAATCTCATCAAATATGATGCTACAAGACAAGCAATTCAATTACCTTTTTTGAATGAA
GTAATTCCTGAAGGGACAGCTGTTATAACTTCTGGTTGGGGACTAACACAAAATTTTAAT
GAATCAAGTTATGTTTTACGAATGGTTGAACTTAAAGTAACAAATCAAGCACAATGTAAT
ATTATATTTTTAGGAGATGGTGGAATTACAACTCGTATGCTTTGTGCTGGTGCTGATGGA
AAAGACAGTTGTGAAGGAGATAGTGGTGGACCGCTTCAACATGCTGTTTCAAAAAAACTT
GTTGGAATAGTCTCATTTGGGCAATCAGGTGGTTGTGCTCAAAAAGGAATACCAGGTGTT
TACACAAGAGTTGCAGCAATAAGAACTTGGATACGCGAAATTGTCGAAATTTAA

>g4558.t4 Gene=g4558 Length=257
MRSLWLILIFVLSALISKCNSREARAISGRIVGGVEVDIEKIPYQVSLLYYDSLACGASI
LSCKFVLTAAHYLLKICLIIVRAGSSTFFEGGSIHDVSKIDIHPQYNRTLLDYDAAILTL
RNLIKYDATRQAIQLPFLNEVIPEGTAVITSGWGLTQNFNESSYVLRMVELKVTNQAQCN
IIFLGDGGITTRMLCAGADGKDSCEGDSGGPLQHAVSKKLVGIVSFGQSGGCAQKGIPGV
YTRVAAIRTWIREIVEI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g4558.t4 CDD cd00190 Tryp_SPc 31 254 2.53669E-73
9 g4558.t4 Gene3D G3DSA:2.40.10.10 - 23 256 7.4E-59
2 g4558.t4 PANTHER PTHR24276 POLYSERASE-RELATED 20 255 2.0E-70
3 g4558.t4 PANTHER PTHR24276:SF83 GH13245P2-RELATED 20 255 2.0E-70
6 g4558.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 57 72 1.6E-8
4 g4558.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 110 124 1.6E-8
5 g4558.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 201 213 1.6E-8
1 g4558.t4 Pfam PF00089 Trypsin 31 251 5.3E-49
11 g4558.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
12 g4558.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
13 g4558.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 16 -
14 g4558.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
10 g4558.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 257 -
17 g4558.t4 ProSitePatterns PS00135 Serine proteases, trypsin family, serine active site. 202 213 -
18 g4558.t4 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 31 256 28.642
16 g4558.t4 SMART SM00020 trypsin_2 30 251 7.6E-71
7 g4558.t4 SUPERFAMILY SSF50494 Trypsin-like serine proteases 14 256 5.83E-69
8 g4558.t4 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -

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:0004252 serine-type endopeptidase activity MF
GO:0006508 proteolysis BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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