General information for g16255.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein ROP.
Parent gene
- The parent gene g16255 is located on chr_4: 8864620..8867161 (+ 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_4 | g16255 | g16255.t1 | isoform | g16255.t1 | 8864620 | 8867161 |
| chr_4 | g16255 | g16255.t1 | exon | g16255.t1.exon1 | 8864620 | 8864647 |
| chr_4 | g16255 | g16255.t1 | cds | g16255.t1.CDS1 | 8864620 | 8864647 |
| chr_4 | g16255 | g16255.t1 | exon | g16255.t1.exon2 | 8864714 | 8864863 |
| chr_4 | g16255 | g16255.t1 | cds | g16255.t1.CDS2 | 8864714 | 8864863 |
| chr_4 | g16255 | g16255.t1 | exon | g16255.t1.exon3 | 8864917 | 8864986 |
| chr_4 | g16255 | g16255.t1 | cds | g16255.t1.CDS3 | 8864917 | 8864986 |
| chr_4 | g16255 | g16255.t1 | exon | g16255.t1.exon4 | 8865047 | 8865132 |
| chr_4 | g16255 | g16255.t1 | cds | g16255.t1.CDS4 | 8865047 | 8865132 |
| chr_4 | g16255 | g16255.t1 | exon | g16255.t1.exon5 | 8865202 | 8865305 |
| chr_4 | g16255 | g16255.t1 | cds | g16255.t1.CDS5 | 8865202 | 8865305 |
| chr_4 | g16255 | g16255.t1 | exon | g16255.t1.exon6 | 8865546 | 8866166 |
| chr_4 | g16255 | g16255.t1 | cds | g16255.t1.CDS6 | 8865546 | 8866166 |
| chr_4 | g16255 | g16255.t1 | exon | g16255.t1.exon7 | 8866257 | 8866538 |
| chr_4 | g16255 | g16255.t1 | cds | g16255.t1.CDS7 | 8866257 | 8866538 |
| chr_4 | g16255 | g16255.t1 | exon | g16255.t1.exon8 | 8866757 | 8867161 |
| chr_4 | g16255 | g16255.t1 | cds | g16255.t1.CDS8 | 8866757 | 8867161 |
| chr_4 | g16255 | g16255.t1 | TTS | g16255.t1 | 8868135 | 8868135 |
| chr_4 | g16255 | g16255.t1 | TSS | g16255.t1 | NA | NA |
Sequences
>g16255.t1 Gene=g16255 Length=1746
ATGAGTTTAAAATTTCTCGTTTGTCAAAAATTAATGAATGAAGTCATCAAGAATGAATCA
CAGCATGGTCAAATGTCTTCAAAAGTTGATTGGCGAGTTTTGATTGTCGACAAATTTTCT
ATGAGAATGATTTCATCTTGTCTAACAATGCATGAACTATCAGCTGAAGGAATTACATTG
GTAGAAGATATAAACAAAAAACGTGAACCATTGCAAACTATGGAAGCTGTTTATTTATTA
ACACCTTGTGAAGATTCTATACAGAAATTAATTCAAGATTTTGATGCATCAAATCGACCA
ATTTATAAATCAGCATATGTTTATTTTACTGAAGCAATTTCAGACAGTTTGTTTGATAAA
ATGAAAGGTCAATCTATTGTGAAATTTATGAAAGCTTGTAAAGAAATTAATGTTTCTTTT
TTGCCATGTGAGAAGCAGGTTTTTTCACTTGATTCACCAAATTTCTTTCAATCTTTCTAC
TCATCAAGTCAAAATTCTAAAACTGAAACTATGGAAAAAATTGCTGAACAAATTGCAACA
CTTTGTGCAACTTTGGGTGAATTTCCATCAATTCGCTATCGCAGTGATTGGAATTCAAAT
CTCGAATTATCAGAATTAATTAGGCAAAAATTGGAAGCTTACAAAAATGATGAGCCTAAA
ATGGGTGAAGGACCAGAAACAGCAAAATCAATTTTATTAATTCTCGATCGTGGTTTTGAT
TGTATTTCGCCATTGCTGCATGAATTGACCTTTCAAGCGATGGCTTATGATTTGCTTCCA
ATTTCGAATGATGTTTATAAATACGACAATAAAGAAGTTTTACTTGATGAAAATGATGAA
TTGTGGTGTGCATTACGTCATGAACATATTGCAGTAGTTTCACAAAAAGTCACAACACAT
TTGAAGAATTTTATTGAATCAAAACCAATTTCTTCAACCGATAAAGCATCGATAAGAGAT
CTGTCACAGATGATTAAGAAAATGCCGCAATATCAAAAGGAATTGTCAAAATATGCAACA
CATTTGCAATTGACTGAAGATTGCATGAATGCTTTTCAAGGTAAAATCAAAAGTCTTTGT
AAAATTGAACAAGATCTTGCAATGGGTAAGGACGCTGATGATGAAGAAATTAAAGATCCA
ATGAGTCAAATGGCACCAATTTTACTTGATCCATCAGTGTCTAACAATGACAAAATTCGC
ATAATTTTACTTTACATCATGAATAAAAATGGAGTTTCAAAAGAGAATTTCGAAAAAGTT
GCAACGCATGCCAATTTGGAGAAAAATGAGAGAGAAATTCTTTTGAATTTGAATCATTTG
GGAGTAAATGTTGTCAATAATGGAAACAATCAAAATAAATATCGCATACCGCGCAAAGAA
AGAATATCAGAAAACACTTACCAAATGTCACGTTGGACACCGATTTTGAAAGATATAATG
GAAGACACAATTGACAATAAATTAGATACAAATCATTTTCCATTTCTTATAAACCGAACA
AAACCAACTTTTAGCAGTGTCGCTAAAAGCACTCGTTTTGGTCGATGGCGCGATGAAAAA
GCACAAAAATCTGAAATCCGAAATGTTCCAAGATTGATTGTTTTTATTGTTGGTGGAATG
AGTTATTCTGAAATGAGATGTGCTTATGAAGTAACCAAAGCTTATGAAAATTGGGAAGTT
ATTCTTGGATCAACGCACATTTTGACACCTGAAATATTTTTGAAAAATTTAAGTGAAATT
TCTTAA
>g16255.t1 Gene=g16255 Length=581
MSLKFLVCQKLMNEVIKNESQHGQMSSKVDWRVLIVDKFSMRMISSCLTMHELSAEGITL
VEDINKKREPLQTMEAVYLLTPCEDSIQKLIQDFDASNRPIYKSAYVYFTEAISDSLFDK
MKGQSIVKFMKACKEINVSFLPCEKQVFSLDSPNFFQSFYSSSQNSKTETMEKIAEQIAT
LCATLGEFPSIRYRSDWNSNLELSELIRQKLEAYKNDEPKMGEGPETAKSILLILDRGFD
CISPLLHELTFQAMAYDLLPISNDVYKYDNKEVLLDENDELWCALRHEHIAVVSQKVTTH
LKNFIESKPISSTDKASIRDLSQMIKKMPQYQKELSKYATHLQLTEDCMNAFQGKIKSLC
KIEQDLAMGKDADDEEIKDPMSQMAPILLDPSVSNNDKIRIILLYIMNKNGVSKENFEKV
ATHANLEKNEREILLNLNHLGVNVVNNGNNQNKYRIPRKERISENTYQMSRWTPILKDIM
EDTIDNKLDTNHFPFLINRTKPTFSSVAKSTRFGRWRDEKAQKSEIRNVPRLIVFIVGGM
SYSEMRCAYEVTKAYENWEVILGSTHILTPEIFLKNLSEIS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g16255.t1 | Gene3D | G3DSA:3.40.50.2060 | - | 1 | 135 | 0 |
| 6 | g16255.t1 | Gene3D | G3DSA:3.40.50.1910 | - | 138 | 578 | 0 |
| 8 | g16255.t1 | Gene3D | G3DSA:3.90.830.10 | Syntaxin Binding Protein 1; Chain A | 248 | 353 | 0 |
| 5 | g16255.t1 | Gene3D | G3DSA:1.25.40.60 | - | 354 | 473 | 0 |
| 2 | g16255.t1 | PANTHER | PTHR11679:SF35 | SYNTAXIN-BINDING PROTEIN 1 | 7 | 578 | 0 |
| 3 | g16255.t1 | PANTHER | PTHR11679 | VESICLE PROTEIN SORTING-ASSOCIATED | 7 | 578 | 0 |
| 9 | g16255.t1 | PIRSF | PIRSF005715 | VPS45_Sec1 | 1 | 581 | 0 |
| 1 | g16255.t1 | Pfam | PF00995 | Sec1 family | 32 | 575 | 0 |
| 4 | g16255.t1 | SUPERFAMILY | SSF56815 | Sec1/munc18-like (SM) proteins | 1 | 579 | 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 K15292 (syntaxin-binding protein 1)
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.
