General information for g6817.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g6817 is located on chr_2: 18881607..18882705 (+ 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 | g6817 | g6817.t1 | TSS | g6817.t1 | 18881398 | 18881398 |
| chr_2 | g6817 | g6817.t1 | isoform | g6817.t1 | 18881607 | 18882705 |
| chr_2 | g6817 | g6817.t1 | exon | g6817.t1.exon1 | 18881607 | 18881916 |
| chr_2 | g6817 | g6817.t1 | cds | g6817.t1.CDS1 | 18881607 | 18881916 |
| chr_2 | g6817 | g6817.t1 | exon | g6817.t1.exon2 | 18881983 | 18882145 |
| chr_2 | g6817 | g6817.t1 | cds | g6817.t1.CDS2 | 18881983 | 18882145 |
| chr_2 | g6817 | g6817.t1 | exon | g6817.t1.exon3 | 18882212 | 18882440 |
| chr_2 | g6817 | g6817.t1 | cds | g6817.t1.CDS3 | 18882212 | 18882440 |
| chr_2 | g6817 | g6817.t1 | exon | g6817.t1.exon4 | 18882502 | 18882705 |
| chr_2 | g6817 | g6817.t1 | cds | g6817.t1.CDS4 | 18882502 | 18882705 |
| chr_2 | g6817 | g6817.t1 | TTS | g6817.t1 | 18882836 | 18882836 |
Sequences
>g6817.t1 Gene=g6817 Length=906
ATGAATCAAACAAAAATTCCTATAAAAGTTGCAGAAATTTCCATAAATAAATTCAATGAA
CAAATTTTTCAAAAAGTCACACAATTAAGAACCTTTCGAATTTCTCAATCAAACACAACG
TCCTTGAGTGATCTAGAGAAATTACGGAAAGATGCAATCAATTGTTTACGCGTTGTGAAA
CAACTTAAGCAGCTCCTAATCGAAATAGATCACCTAAAATCACAAACAAGAGAAGAAGAT
CATGAAAAATTTGATGAATTAACATCACGGAGACGACAAGATGCACTAAAAGAAATTCAA
TTATATCAAGATATGAAACCTATAGATAAACTTAACGAATTATCACATCATGCGACAACT
AATATTGATAATGAAATGCCAGCAATTGATACAAAGAAAGAAAACATTCACATACAGCTT
CAAGTAGATGATCGAGAAATCAGAAAACGCGAATTGGAATCAAGAGAAGCATTATTGAGG
GAATTTGAGAATTTACAAACTGAATGTGAATCAATTGCAAATTTATTTCAAAATGTCAGT
GAACTGGTAGCAGAGCAGGCACCTATGGTTGATAAGATTGAAGAAAATGTTGAAGAAACA
GAACATAATGTTGAAGAAGGTACAAAACATTTACAGCAAGCATTAAGTTATAAGAAAACT
ATGTATCCACTTCTTGGTGGACTTGTAGGAGCTGCCATGCTAGGACCTGTTGGATTAATA
GCAGGTTTAAAAGCAGGATCAGCTGCAACACTTTGTGGTGGAATATGTGGTTATGCTGGA
GGTAAGATTCTCAAAAAAGCAAATACTCCTACTGAATCATTAATACCAAATAGTGATGAA
ATTAATGATACGCACAAGATGTCAAAAGAACAGCAAAGCGAAGATAATTTAAAGGCTTTA
TCATAA
>g6817.t1 Gene=g6817 Length=301
MNQTKIPIKVAEISINKFNEQIFQKVTQLRTFRISQSNTTSLSDLEKLRKDAINCLRVVK
QLKQLLIEIDHLKSQTREEDHEKFDELTSRRRQDALKEIQLYQDMKPIDKLNELSHHATT
NIDNEMPAIDTKKENIHIQLQVDDREIRKRELESREALLREFENLQTECESIANLFQNVS
ELVAEQAPMVDKIEENVEETEHNVEEGTKHLQQALSYKKTMYPLLGGLVGAAMLGPVGLI
AGLKAGSAATLCGGICGYAGGKILKKANTPTESLIPNSDEINDTHKMSKEQQSEDNLKAL
S
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6817.t1 | Coils | Coil | Coil | 148 | 175 | - |
| 7 | g6817.t1 | Coils | Coil | Coil | 190 | 210 | - |
| 6 | g6817.t1 | Gene3D | G3DSA:1.20.5.110 | - | 141 | 238 | 3.2E-14 |
| 11 | g6817.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 274 | 301 | - |
| 2 | g6817.t1 | PANTHER | PTHR19957 | SYNTAXIN | 2 | 259 | 2.2E-39 |
| 3 | g6817.t1 | PANTHER | PTHR19957:SF139 | SYNTAXIN-17 | 2 | 259 | 2.2E-39 |
| 1 | g6817.t1 | Pfam | PF05739 | SNARE domain | 189 | 219 | 1.9E-8 |
| 12 | g6817.t1 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 171 | 214 | 12.8 |
| 10 | g6817.t1 | SMART | SM00397 | tSNARE_6 | 147 | 214 | 1.4E-6 |
| 5 | g6817.t1 | SUPERFAMILY | SSF47661 | t-snare proteins | 15 | 207 | 4.39E-11 |
| 4 | g6817.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 152 | 219 | 6.02E-13 |
| 9 | g6817.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 221 | 243 | - |
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:0016020 | membrane | CC |
| GO:0000149 | SNARE binding | MF |
| GO:0097352 | autophagosome maturation | BP |
| GO:0097111 | endoplasmic reticulum-Golgi intermediate compartment organization | BP |
| GO:0006888 | endoplasmic reticulum to Golgi vesicle-mediated transport | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K08491 (syntaxin 17)
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.
