General information for g5002.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Chymotrypsin BII.
Parent gene
- The parent gene g5002 is located on chr_2: 6388991..6390996 (+ 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 | g5002 | g5002.t1 | isoform | g5002.t1 | 6388991 | 6390996 |
| chr_2 | g5002 | g5002.t1 | exon | g5002.t1.exon1 | 6388991 | 6389306 |
| chr_2 | g5002 | g5002.t1 | cds | g5002.t1.CDS1 | 6388991 | 6389306 |
| chr_2 | g5002 | g5002.t1 | exon | g5002.t1.exon2 | 6390427 | 6390570 |
| chr_2 | g5002 | g5002.t1 | cds | g5002.t1.CDS2 | 6390427 | 6390570 |
| chr_2 | g5002 | g5002.t1 | exon | g5002.t1.exon3 | 6390629 | 6390781 |
| chr_2 | g5002 | g5002.t1 | cds | g5002.t1.CDS3 | 6390629 | 6390781 |
| chr_2 | g5002 | g5002.t1 | exon | g5002.t1.exon4 | 6390842 | 6390996 |
| chr_2 | g5002 | g5002.t1 | cds | g5002.t1.CDS4 | 6390842 | 6390996 |
| chr_2 | g5002 | g5002.t1 | TSS | g5002.t1 | NA | NA |
| chr_2 | g5002 | g5002.t1 | TTS | g5002.t1 | NA | NA |
Sequences
>g5002.t1 Gene=g5002 Length=768
ATGAAGTTAATAACAACAGTTGTATTCTGTGTTTTAGTATCTTATTCTTACGCAATTCAT
AATGGTCAAGTAGTTCAACCTAATAGCATCCCCTATCAAGTGTTGCTATTAGTTAAAAGA
GGAGATAAGACAAGCAAATGCGGTGGATCACTTGTGAAGCCTGATCGTGTTTTAACAGCT
GCTCATTGTCTTAAAGATCGAGATTCAGTTGAAGTAATTGTTGGAGCACATAAAATACAT
GATAGACGTGAAAAAACACGACAGTCGCAGACAGTTGAACCTAGTAATCTGTTTCCACAT
CCAACATGGGCACCTGGTAAAGGTCATGATGTCGGTATTGTTAAATTGCCAGAACCTTTT
GAATTAAATGAATATGTTGACACAATCAAATTGCCATATGGTCTTGATGATGAATCATTT
AATGGTGAAATTGCAAAAATAGCTGGCTGGGGTGAAATTGATGACAACCCAAGAGATCAT
GTTGGTCCTTTACGTGCAGTTGAAAATCCAATTATTTCAAACCACGACTGTCGTAAACAT
CACGTAAAAATAGATAGTGGAAACTTATGCTTGTCTGAAAAAGGAGGAAGAAGAACTTGC
TCAGGCGATTCAGGTGGTCCACTCGTTGTTCGTTTTAATGGAGAAATCATTCAAGTTGGT
CTTACAAGTAAAGGTGACAGTCATGGTTGTGACACAGTTGCACCTTCAATCTTTACTCGA
GTCACATCATATCTCGATAATTTTATCGATAAACATTTGTCAGAATAA
>g5002.t1 Gene=g5002 Length=255
MKLITTVVFCVLVSYSYAIHNGQVVQPNSIPYQVLLLVKRGDKTSKCGGSLVKPDRVLTA
AHCLKDRDSVEVIVGAHKIHDRREKTRQSQTVEPSNLFPHPTWAPGKGHDVGIVKLPEPF
ELNEYVDTIKLPYGLDDESFNGEIAKIAGWGEIDDNPRDHVGPLRAVENPIISNHDCRKH
HVKIDSGNLCLSEKGGRRTCSGDSGGPLVVRFNGEIIQVGLTSKGDSHGCDTVAPSIFTR
VTSYLDNFIDKHLSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g5002.t1 | CDD | cd00190 | Tryp_SPc | 19 | 252 | 5.34058E-63 |
| 10 | g5002.t1 | Gene3D | G3DSA:2.40.10.10 | - | 21 | 242 | 2.0E-54 |
| 9 | g5002.t1 | Gene3D | G3DSA:2.40.10.10 | - | 31 | 246 | 2.0E-54 |
| 2 | g5002.t1 | PANTHER | PTHR24250:SF56 | SERINE PROTEASE P96 | 7 | 250 | 6.2E-62 |
| 3 | g5002.t1 | PANTHER | PTHR24250 | CHYMOTRYPSIN-RELATED | 7 | 250 | 6.2E-62 |
| 5 | g5002.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 48 | 63 | 4.5E-12 |
| 6 | g5002.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 106 | 120 | 4.5E-12 |
| 4 | g5002.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 197 | 209 | 4.5E-12 |
| 1 | g5002.t1 | Pfam | PF00089 | Trypsin | 19 | 246 | 3.7E-46 |
| 12 | g5002.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 13 | g5002.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 14 | g5002.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 15 | g5002.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 11 | g5002.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 255 | - |
| 18 | g5002.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 58 | 63 | - |
| 19 | g5002.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 19 | 254 | 25.782 |
| 17 | g5002.t1 | SMART | SM00020 | trypsin_2 | 18 | 249 | 2.1E-57 |
| 7 | g5002.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 7 | 246 | 3.14E-57 |
| 8 | g5002.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5002/g5002.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5002.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 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.
