General information for g513.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vitellin-degrading protease.
Parent gene
- The parent gene g513 is located on chr_3: 3853654..3855533 (+ 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_3 | g513 | g513.t1 | TSS | g513.t1 | 3853291 | 3853291 |
| chr_3 | g513 | g513.t1 | isoform | g513.t1 | 3853318 | 3855533 |
| chr_3 | g513 | g513.t1 | exon | g513.t1.exon1 | 3853318 | 3853375 |
| chr_3 | g513 | g513.t1 | cds | g513.t1.CDS1 | 3853318 | 3853375 |
| chr_3 | g513 | g513.t1 | exon | g513.t1.exon2 | 3853656 | 3854097 |
| chr_3 | g513 | g513.t1 | cds | g513.t1.CDS2 | 3853656 | 3854097 |
| chr_3 | g513 | g513.t1 | exon | g513.t1.exon3 | 3854157 | 3854309 |
| chr_3 | g513 | g513.t1 | cds | g513.t1.CDS3 | 3854157 | 3854309 |
| chr_3 | g513 | g513.t1 | exon | g513.t1.exon4 | 3855334 | 3855410 |
| chr_3 | g513 | g513.t1 | cds | g513.t1.CDS4 | 3855334 | 3855410 |
| chr_3 | g513 | g513.t1 | exon | g513.t1.exon5 | 3855472 | 3855533 |
| chr_3 | g513 | g513.t1 | cds | g513.t1.CDS5 | 3855472 | 3855533 |
| chr_3 | g513 | g513.t1 | TTS | g513.t1 | 3855573 | 3855573 |
Sequences
>g513.t1 Gene=g513 Length=792
ATGAAGTTGAAATTCTTTGTATTTTTAGCAATTTTTGCTGTAATTTCTGGTCAAGAAGAT
ATTTTTGTTCCTGACTTTCAATATGACGTAGACACCAATCGTGGACCACGAATAGTTGGT
GGACATGATGCAAATATTGAAGAGGTCCCATATCAAGTTTCACTTCGTCGCTATAATGAA
GAAACTCAACTTTGGGGACACACATGCGGTGGAATCATTCTCACTACTGATGTTACTTTA
AATGCTGCACATTGTGTTTATAATAGACTTCATATGAAATTCCAAATTCGTGCTGGTTCT
GATTTAAGATCACAAGGTGGTCAACTTGTAAATGTTACGAAATTGATCATGCATCCTGAC
TATCAACCAAGTGGATTATATAATGATATTGCTATACTTAAGTTGCAACACAAATTAATA
TTTGGCAGCAAAGTTTGGTCAATTGGTTTGCCACCAAGAGGTTATAGAGTTCCAGATGGT
GCAGCTTTATTAGTTAGCGGCTGGGGAGCATTAGAATGGCAAGGTTCATCACCTGAAAGA
TTGCAAAAAGTTTATGTTCCTGCTGTTTCAAATGAAAAATGTGCTGAAGTTTATGCAAAT
ATTCGTCCTCATAAAATTTGTGCTGGAATTGTTGGAAAAGATTCTTGTCAAGGTGACAGC
GGTGGTCCTTTGGTTTACAAAAATTTCGTTGTTGGAGTTGTTTCATCAGGATATCGTTGT
GCATATGATGGATATCCCGGAATTTACACCAGAGTTTCAGAATTTTTAGATTTTATTGTT
CGAAATTTATAA
>g513.t1 Gene=g513 Length=263
MKLKFFVFLAIFAVISGQEDIFVPDFQYDVDTNRGPRIVGGHDANIEEVPYQVSLRRYNE
ETQLWGHTCGGIILTTDVTLNAAHCVYNRLHMKFQIRAGSDLRSQGGQLVNVTKLIMHPD
YQPSGLYNDIAILKLQHKLIFGSKVWSIGLPPRGYRVPDGAALLVSGWGALEWQGSSPER
LQKVYVPAVSNEKCAEVYANIRPHKICAGIVGKDSCQGDSGGPLVYKNFVVGVVSSGYRC
AYDGYPGIYTRVSEFLDFIVRNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g513.t1 | CDD | cd00190 | Tryp_SPc | 38 | 262 | 1.33963E-86 |
| 9 | g513.t1 | Gene3D | G3DSA:2.40.10.10 | - | 30 | 263 | 1.0E-66 |
| 2 | g513.t1 | PANTHER | PTHR24276 | POLYSERASE-RELATED | 6 | 261 | 1.4E-66 |
| 3 | g513.t1 | PANTHER | PTHR24276:SF78 | AT20289P-RELATED | 6 | 261 | 1.4E-66 |
| 6 | g513.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 70 | 85 | 6.6E-13 |
| 4 | g513.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 125 | 139 | 6.6E-13 |
| 5 | g513.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 213 | 225 | 6.6E-13 |
| 1 | g513.t1 | Pfam | PF00089 | Trypsin | 38 | 259 | 8.2E-58 |
| 11 | g513.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 12 | g513.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 13 | g513.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 12 | - |
| 14 | g513.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 10 | g513.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 263 | - |
| 17 | g513.t1 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 214 | 225 | - |
| 18 | g513.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 38 | 263 | 30.883 |
| 16 | g513.t1 | SMART | SM00020 | trypsin_2 | 37 | 259 | 7.1E-80 |
| 7 | g513.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 7 | 262 | 1.09E-74 |
| 8 | g513.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g513/g513.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g513.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 K01312 (trypsin)
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