General information for g5534.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
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.t16 | TTS | g5534.t16 | 10126405 | 10126405 |
| chr_2 | g5534 | g5534.t16 | isoform | g5534.t16 | 10126447 | 10128867 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon1 | 10126447 | 10126628 |
| chr_2 | g5534 | g5534.t16 | cds | g5534.t16.CDS1 | 10126447 | 10126628 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon2 | 10126699 | 10126862 |
| chr_2 | g5534 | g5534.t16 | cds | g5534.t16.CDS2 | 10126699 | 10126849 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon3 | 10126920 | 10126955 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon4 | 10127012 | 10127232 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon5 | 10127297 | 10127346 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon6 | 10127478 | 10127569 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon7 | 10127629 | 10127759 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon8 | 10127837 | 10128055 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon9 | 10128130 | 10128230 |
| chr_2 | g5534 | g5534.t16 | exon | g5534.t16.exon10 | 10128667 | 10128867 |
| chr_2 | g5534 | g5534.t16 | TSS | g5534.t16 | NA | NA |
Sequences
>g5534.t16 Gene=g5534 Length=1397
TCTTATTATAGTTTTAAGTAGTTTTTAATAAAAACACTTTAAGATTTCTTCTTAAAAATT
AAAAATTGAAAAATAAAGTCTGATCTCAGAATCAGTTGTAGACTTTTCTACAACATAAAT
TTTATATTGTAGAAATTTGAATTTAACCGTTTTGATTTTTTGAAATTTTTTAAACGTTCA
GTTGATTGATGAGTTACATTTTGTCGAAATGTTCGTGATTAAAATGAAATTTTTAACTTT
TAATCTAAATATTTTAATCATCATTGTTCTGTCAAATTTAATATTGATTGAGTCACTCGA
AGTCCTTGTACGAGTTTTGATAATTCTCCAGGAGTTTGTAAAGTTTTGTCACAATGCAAC
TGGGCAGTTGATAAGATTAAATCTAAAGAAATTGCAATTGGACAATTGATTAGATGTGGT
TTTAAAAATCGAGATGTGATTATTTGTTGCAAACATAATGTTGCTCCGCCATTAGAATTA
GTTGTGAACACTAAAAGTCCAGCATCTACAACAGTGTATGGTGAAGACAGACCTCCAGTT
TTCGTAACGTTTCAATCACAAAGAAAATCAATACAGGCATGTGAACAAATTAAAAAAATT
GTTCCAATTGGTGTTCAATTCAATATAATTGGCGGTGAACAGGCTGAAAAAGGAGAATTT
CCGCATCAAGTTGTGTTAGGATATCCCGATGAATTAGACCCAAATAAAATTTCATACGAT
TGTGGTGGAAGTTTAATATCAAAGAATCATTTACAGCTCATTGCGTCAATAACCGACAAC
GACAACCAAGTGTTATTTTACTTGGCAAGACATCCTTAAATGATGATGATGAACTTGATC
CAATTTTAATACCAGTTAAAAAAATAATAATTCATTCCAATTATACATCTAGACGAAAAT
ATGACGATATTGCTTTGATTGAATTAGAACATAACGTAGAAAAATATAACTATTATGTTA
AACCAGCTTGCCTTTATACAAAGCATACAATCTTAACTGAAATTGCAATCATCACAGGAT
TTGGCATTGTTAATCAAGAAACAAGGAGAAAATCTGATTGGCTAATGAAAGCAGATGTAA
CTGAAGTGCCGTTGACTGATTGTAGAGAAAAATATGCAACGACTGGTTTATCAAGAATTC
CAGATAATTTAAGACAGACACAAATGTGCGCTACTGGTATAAATAGTGCCGGCACAACTA
TTGATGCATGTCAAGGTGATAGCGGAGGTCCGATTCAAATAAAGGAGTTATACAAGGGAG
AAAAATATTATACAGTTGTGGGAGTGACAAGTTTTGGAGCAAGCTGTGGAAGTCAAATTC
CAGGTGTATATACTCGAGTATCTGAATACTTAGATTGGATTGAACCAATTGTTTGGCCTA
GTAATGTAGTCATTTAA
>g5534.t16 Gene=g5534 Length=110
MKADVTEVPLTDCREKYATTGLSRIPDNLRQTQMCATGINSAGTTIDACQGDSGGPIQIK
ELYKGEKYYTVVGVTSFGASCGSQIPGVYTRVSEYLDWIEPIVWPSNVVI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5534.t16 | Gene3D | G3DSA:2.40.10.10 | - | 1 | 104 | 1.9E-26 |
| 2 | g5534.t16 | PANTHER | PTHR24260 | - | 5 | 107 | 2.4E-26 |
| 3 | g5534.t16 | PANTHER | PTHR24260:SF91 | FI18411P1-RELATED | 5 | 107 | 2.4E-26 |
| 1 | g5534.t16 | Pfam | PF00089 | Trypsin | 4 | 99 | 9.6E-17 |
| 5 | g5534.t16 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 47 | 58 | - |
| 7 | g5534.t16 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 1 | 104 | 11.8 |
| 4 | g5534.t16 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 2 | 104 | 1.02E-26 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5534/g5534.t16; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5534.t16.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 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.
