General information for g5534.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Serine protease persephone.
Parent gene
- The parent gene g5534 is located on chr_2: 10128055..10128867 (- 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 | g5534 | g5534.t1 | TTS | g5534.t1 | 10126405 | 10126405 |
| chr_2 | g5534 | g5534.t1 | isoform | g5534.t1 | 10126447 | 10128208 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon1 | 10126447 | 10126628 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS1 | 10126447 | 10126628 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon2 | 10126699 | 10126862 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS2 | 10126699 | 10126862 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon3 | 10126920 | 10126955 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS3 | 10126920 | 10126955 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon4 | 10127012 | 10127232 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS4 | 10127012 | 10127232 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon5 | 10127297 | 10127334 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS5 | 10127297 | 10127334 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon6 | 10127397 | 10127415 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS6 | 10127397 | 10127415 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon7 | 10127478 | 10127569 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS7 | 10127478 | 10127569 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon8 | 10127629 | 10127759 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS8 | 10127629 | 10127759 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon9 | 10127837 | 10128062 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS9 | 10127837 | 10128062 |
| chr_2 | g5534 | g5534.t1 | exon | g5534.t1.exon10 | 10128130 | 10128208 |
| chr_2 | g5534 | g5534.t1 | cds | g5534.t1.CDS10 | 10128130 | 10128208 |
| chr_2 | g5534 | g5534.t1 | TSS | g5534.t1 | 10128343 | 10128343 |
Sequences
>g5534.t1 Gene=g5534 Length=1188
ATGAAATTTTTAACTTTTAATCTAAATATTTTAATCATCATTGTTCTGTCAAATTTAATA
TTGATTGAGTCACTCGAAGAGGGAAGTCCTTGTACGAGTTTTGATAATTCTCCAGGAGTT
TGTAAAGTTTTGTCACAATGCAACTGGGCAGTTGATAAGATTAAATCTAAAGAAATTGCA
ATTGGACAATTGATTAGATGTGGTTTTAAAAATCGAGATGTGATTATTTGTTGCAAACAT
AATGTTGCTCCGCCATTAGAATTAGTTGTGAACACTAAAAGTCCAGCATCTACAACAGTG
TATGGTGAAGACAGACCTCCAGTTTTCGTAACGTTTCAATCACAAAGAAAATCAATACAG
GCATGTGAACAAATTAAAAAAATTGTTCCAATTGGTGTTCAATTCAATATAATTGGCGGT
GAACAGGCTGAAAAAGGAGAATTTCCGCATCAAGTTGTGTTAGGATATCCCGATGAATTA
GACCCAAATAAAATTTCATACGATTGTGGTGGAAGTTTAATATCAAAGAATTTTATATTA
ACTGCCGCTCATTGCGTCAATAACCGACAACGACAACCAAGTGTTATTTTACTTGGCAAG
ACATCCTTAAATGATGATGATGAACTTGATCCAATTTTAATACCAGTTAAAAAAATAATA
ATTCATTCCAATTATACATCTAGACGAAAATATGACGATATTGCTTTGATTGAATTAGAA
CATAACGTAGAAAAATATAACTATTATGTTAAACCAGCTTGCCTTTATACAAAGCATACA
ATCTTAACTGAAATTGCAATCATCACAGGATTTGGCATTGTTAATCAAGAAACAAGGAGA
AAATCTGATTGGCTAATGAAAGCAGATGTAACTGAAGTGCCGTTGACTGATTGTAGAGAA
AAATATGCAACGACTGGTTTATCAAGAATTCCAGATAATTTAAGACAGACACAAATGTGC
GCTACTGGTATAAATAGTGCCGGCACAACTATTGATGCATGTCAAGGTGATAGCGGAGGT
CCGATTCAAATAAAGGAGTTATACAAGGGAGAAAAATATTATACAGTTGTGGGAGTGACA
AGTTTTGGAGCAAGCTGTGGAAGTCAAATTCCAGGTGTATATACTCGAGTATCTGAATAC
TTAGATTGGATTGAACCAATTGTTTGGCCTAGTAATGTAGTCATTTAA
>g5534.t1 Gene=g5534 Length=395
MKFLTFNLNILIIIVLSNLILIESLEEGSPCTSFDNSPGVCKVLSQCNWAVDKIKSKEIA
IGQLIRCGFKNRDVIICCKHNVAPPLELVVNTKSPASTTVYGEDRPPVFVTFQSQRKSIQ
ACEQIKKIVPIGVQFNIIGGEQAEKGEFPHQVVLGYPDELDPNKISYDCGGSLISKNFIL
TAAHCVNNRQRQPSVILLGKTSLNDDDELDPILIPVKKIIIHSNYTSRRKYDDIALIELE
HNVEKYNYYVKPACLYTKHTILTEIAIITGFGIVNQETRRKSDWLMKADVTEVPLTDCRE
KYATTGLSRIPDNLRQTQMCATGINSAGTTIDACQGDSGGPIQIKELYKGEKYYTVVGVT
SFGASCGSQIPGVYTRVSEYLDWIEPIVWPSNVVI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g5534.t1 | CDD | cd00190 | Tryp_SPc | 137 | 385 | 4.95716E-68 |
| 9 | g5534.t1 | Gene3D | G3DSA:2.40.10.10 | - | 137 | 377 | 2.6E-65 |
| 10 | g5534.t1 | Gene3D | G3DSA:2.40.10.10 | - | 149 | 385 | 2.6E-65 |
| 2 | g5534.t1 | PANTHER | PTHR24260:SF107 | EG:BACR7A4.3 PROTEIN-RELATED | 12 | 392 | 5.8E-76 |
| 3 | g5534.t1 | PANTHER | PTHR24260 | - | 12 | 392 | 5.8E-76 |
| 6 | g5534.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 170 | 185 | 9.7E-13 |
| 5 | g5534.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 229 | 243 | 9.7E-13 |
| 4 | g5534.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 331 | 343 | 9.7E-13 |
| 1 | g5534.t1 | Pfam | PF00089 | Trypsin | 137 | 384 | 1.9E-48 |
| 12 | g5534.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 28 | - |
| 13 | g5534.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 14 | g5534.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 21 | - |
| 15 | g5534.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 22 | 28 | - |
| 11 | g5534.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 29 | 395 | - |
| 18 | g5534.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 180 | 185 | - |
| 19 | g5534.t1 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 332 | 343 | - |
| 21 | g5534.t1 | ProSiteProfiles | PS51888 | Clip domain profile. | 30 | 78 | 8.739 |
| 20 | g5534.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 137 | 389 | 27.162 |
| 17 | g5534.t1 | SMART | SM00020 | trypsin_2 | 136 | 384 | 1.7E-63 |
| 7 | g5534.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 118 | 389 | 4.47E-71 |
| 8 | g5534.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5534/g5534.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5534.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004252 | serine-type endopeptidase activity | MF |
| GO:0006508 | proteolysis | BP |
KEGG
Orthology
- This transcript has been annotated with K20671 (serine protease persephone [EC:3.4.21.-])
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. There were no conditions that were differentially expressed