General information for g4087.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 45.
Parent gene
- The parent gene g4087 is located on chr_3: 30512401..30513633 (+ 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 | g4087 | g4087.t1 | TSS | g4087.t1 | 30510554 | 30510554 |
| chr_3 | g4087 | g4087.t1 | isoform | g4087.t1 | 30510615 | 30512401 |
| chr_3 | g4087 | g4087.t1 | exon | g4087.t1.exon1 | 30510615 | 30510707 |
| chr_3 | g4087 | g4087.t1 | cds | g4087.t1.CDS1 | 30510615 | 30510707 |
| chr_3 | g4087 | g4087.t1 | exon | g4087.t1.exon2 | 30510773 | 30512401 |
| chr_3 | g4087 | g4087.t1 | cds | g4087.t1.CDS2 | 30510773 | 30512401 |
| chr_3 | g4087 | g4087.t1 | TTS | g4087.t1 | NA | NA |
Sequences
>g4087.t1 Gene=g4087 Length=1722
ATGAATCTAATTAAAGCAGTTCAAATGTATATCGATAAAATGATAGAAGAGGCAGGAGTA
GGAATGAAAATACTATTGATGGATCGTGAAACCACATCAATAATATCAATGGCATTCTCT
CAAACAGAAATGCTTCAGAAAGAAGTGTATTTATTTGAACGTATTGATTCTGGCAGATCC
AATGAAAGATTAAAATATTTGAAATGTATCGTTTTTATTCGTCCTACAAGAGAAAACATT
CTTCGCTTGTCAAATGAACTTAAATCGCCAAAATATGGATCATATTTTATATACTTTAGC
AACATTATTCCAAGAACTGATATCAAAGCATTAGCAGAATGTGATGAAAGTGAATCCGTA
CGAGAAGTCAAAGAAGTCTATGCAGATTTTTTAAGCATCAATGCTAATCTCTTTTCAATT
AACATTCCAACTTGCTTACATGCTTTAAATTGGCAATCTGATGCTCTTGATAGATCAGTG
AGCGGAATTATAGGTGTTTTGTTATCATTAAAAATAAGACCAACAATTAGATACAAAATT
GGAAGTCAAGTGGCTCAAACACTTGCCAAACGAGTTTTTGACACAATCAACAAAGAGAGC
TCACTATTTAGCTTTCGTCCACCCGAAAATGGCATCCCTCCTCCTTTACTTTTGATTCTT
GATCGATGTGATGATCCAATTACTCCTCTACTAACACAATGGACTTATCAAGCTATGGTA
CATCAATTGCTAACAATAAAAAATAATCGTGTTGATCTCTCTAATGTAGCTGGAGTGCCG
AGTGAGCTTAAGGAAGTAGTTCTCTCAGCTGAACAAGATGACTTTTATGCTAAGAATTTA
TTTTCAAACTATGGCGAGATTGCAACAACAATTCGAGATTTAATTGAATCATTTCAGAAG
CGTGCAAAAGAACAAAAAAAAATTGAAACTATTGCAGATATGAAAAATTTTGTCGAAACT
TATCCACAATTCAAAAAAATGTCTGGAACTGTTAATAAACATTTAGTTTTAATCAGTGAA
CTGTCAATGAAAATTGGAAAAAGGTCTCTACTTGAGTTATCTGAATTAGAGCAAGATATG
GTTTGCAAACCAGATCATTCTGCTCAATTACAGAAAATTAAAAAGCTCGTTTCAGAAGAA
AGAATTAATGTTGAAGATGCATTGCGTTTAATTTTAATGTATTCAATGCGATATGAACGA
CATGCAAATTGTGGAACTGTTGGTCTCTTAAATTCACTAAAAGAAAGAAATGGAAGAACT
CATTTAGTGCCAAAGATGCTCGAGTATATAAGTCAATCGGCAAGGTCAGAACTTTTTAAT
ACAGTAAAAATTACCGATGCTGTAAAATTAACAAGAAACTTAATCAAAGGATTGAAAGGA
ATAGAAAATGTTTATACACAGCATGTTTGTGTATTGAAAGAGTTGCTTGAAGAAATTTTT
AAAGGTCGACCAATTGATCAACAATATCCATTTATTAATTCATCAGAAGTTCCTTATAGG
CGACCACCGACAGAAATTATTGTTTTTATAGTTGGTGGTGCCACATATGAAGAAGCTTTG
GCAGTTCATCAACTTAATCAATTGGGTTATCGTGTTATATTAGGAGGCACAACTATTCAT
AATTCTGAAACTTTCCTAGAAGAAGTTATTGCAGCAACAAATGGAGCACCTTTTAAACAT
TCCCGATCACTGCAAGCTTTTCATAATGCATCAAATGCCTAA
>g4087.t1 Gene=g4087 Length=573
MNLIKAVQMYIDKMIEEAGVGMKILLMDRETTSIISMAFSQTEMLQKEVYLFERIDSGRS
NERLKYLKCIVFIRPTRENILRLSNELKSPKYGSYFIYFSNIIPRTDIKALAECDESESV
REVKEVYADFLSINANLFSINIPTCLHALNWQSDALDRSVSGIIGVLLSLKIRPTIRYKI
GSQVAQTLAKRVFDTINKESSLFSFRPPENGIPPPLLLILDRCDDPITPLLTQWTYQAMV
HQLLTIKNNRVDLSNVAGVPSELKEVVLSAEQDDFYAKNLFSNYGEIATTIRDLIESFQK
RAKEQKKIETIADMKNFVETYPQFKKMSGTVNKHLVLISELSMKIGKRSLLELSELEQDM
VCKPDHSAQLQKIKKLVSEERINVEDALRLILMYSMRYERHANCGTVGLLNSLKERNGRT
HLVPKMLEYISQSARSELFNTVKITDAVKLTRNLIKGLKGIENVYTQHVCVLKELLEEIF
KGRPIDQQYPFINSSEVPYRRPPTEIIVFIVGGATYEEALAVHQLNQLGYRVILGGTTIH
NSETFLEEVIAATNGAPFKHSRSLQAFHNASNA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4087.t1 | Gene3D | G3DSA:3.40.50.2060 | - | 1 | 128 | 0 |
| 6 | g4087.t1 | Gene3D | G3DSA:3.40.50.1910 | - | 136 | 549 | 0 |
| 8 | g4087.t1 | Gene3D | G3DSA:3.90.830.10 | Syntaxin Binding Protein 1; Chain A | 233 | 347 | 0 |
| 5 | g4087.t1 | Gene3D | G3DSA:1.25.40.60 | - | 348 | 469 | 0 |
| 2 | g4087.t1 | PANTHER | PTHR11679:SF3 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 | 3 | 550 | 0 |
| 3 | g4087.t1 | PANTHER | PTHR11679 | VESICLE PROTEIN SORTING-ASSOCIATED | 3 | 550 | 0 |
| 9 | g4087.t1 | PIRSF | PIRSF005715 | VPS45_Sec1 | 1 | 557 | 0 |
| 1 | g4087.t1 | Pfam | PF00995 | Sec1 family | 23 | 548 | 0 |
| 4 | g4087.t1 | SUPERFAMILY | SSF56815 | Sec1/munc18-like (SM) proteins | 1 | 550 | 0 |
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:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K12479 (vacuolar protein sorting-associated protein 45)
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.
