General information for g13187.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Syntaxin-16.
Parent gene
- The parent gene g13187 is located on chr_1: 28390867..28391230 (+ 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_1 | g13187 | g13187.t1 | TSS | g13187.t1 | 28390046 | 28390046 |
| chr_1 | g13187 | g13187.t1 | isoform | g13187.t1 | 28390133 | 28391230 |
| chr_1 | g13187 | g13187.t1 | exon | g13187.t1.exon1 | 28390133 | 28390207 |
| chr_1 | g13187 | g13187.t1 | cds | g13187.t1.CDS1 | 28390133 | 28390207 |
| chr_1 | g13187 | g13187.t1 | exon | g13187.t1.exon2 | 28390271 | 28391230 |
| chr_1 | g13187 | g13187.t1 | cds | g13187.t1.CDS2 | 28390271 | 28391230 |
| chr_1 | g13187 | g13187.t1 | TTS | g13187.t1 | 28391315 | 28391315 |
Sequences
>g13187.t1 Gene=g13187 Length=1035
ATGGCGACTCGTTATTTGACAGAATTGTTCTCATTGATGAGAAATTCTCACAGTTATAGA
AATAGTCATTTTTCTAAAGGCGGTGATAATGAACGGCTGCTGAAAAGTAAGAATTCTGGA
TCAGATGAAGAAGTTGAATTAAATGATGAATATGTATCACTTCCACAATGGGCAGATACT
GTTGAAAATACAAAGTATACAATTTCCAAAATTGCTTCAAAACAAGCAGAATTGGAAGTT
TTACATAAAAAACTTTTAAGACCTGAGTTTATAGAGAAAAGCAACGATGAGATTCAAATG
GAGCAGTTAGGTCAAGAAATTTCAAAGTTAATAGGCATTGCTCATAAGAATATTTTAACA
ATCAAGTCACATCAATATGCTACAAGTTCAGCACTCGAGCGAAAGTTGATTGAACATGTT
TGTAAAGGACTTTGTGGCACTCTTCAGACTCAAACTGCAAGCTTTAGAAATGAACAAAAC
ACTTATCTCAAACAAATTAACCAAATGGAAGAATACACAAATGAATTCTTTGACTCATTG
AACTTTAATGGCACCAATGATGATAAGACTGTAGATTCGTTTGATAATTTTCTTAAACCA
ACAACATCAACGATCACCAATAGTAATGGCTTCAACCATAGTCAATTGGATGACTTAGAT
AATGATGAGAGATTAGATGAATATTTTCAAATTAAGCCAAATCAAAAGTTCAATCAGCAA
CATTTACTTCGTTTAGAAGTTGATAACACAAAATTAGTTGAAGCACGAGAAAAAGAGGTG
ATGAATATTGTGAAATCAATTGTGGATCTTAATCAAATTTACAAGGATTTATCGCATCTA
GTTGAAGAGCAAGGTACTGTTTTAGATAGAATCGATTATAATATTGAATCAACTCAAACA
CGCGTATATGAGGGCTACAAACAACTGCAAAAAGCTGAACGCTATCAACGTGCAAATAGA
AAAATGTATTGCATATTTATTTTAGCCTCTGTGACATTGTTTATGATCATATTACTTATT
ATCGTAAAACTATAA
>g13187.t1 Gene=g13187 Length=344
MATRYLTELFSLMRNSHSYRNSHFSKGGDNERLLKSKNSGSDEEVELNDEYVSLPQWADT
VENTKYTISKIASKQAELEVLHKKLLRPEFIEKSNDEIQMEQLGQEISKLIGIAHKNILT
IKSHQYATSSALERKLIEHVCKGLCGTLQTQTASFRNEQNTYLKQINQMEEYTNEFFDSL
NFNGTNDDKTVDSFDNFLKPTTSTITNSNGFNHSQLDDLDNDERLDEYFQIKPNQKFNQQ
HLLRLEVDNTKLVEAREKEVMNIVKSIVDLNQIYKDLSHLVEEQGTVLDRIDYNIESTQT
RVYEGYKQLQKAERYQRANRKMYCIFILASVTLFMIILLIIVKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g13187.t1 | CDD | cd15845 | SNARE_syntaxin16 | 253 | 311 | 5.75215E-25 |
| 6 | g13187.t1 | Gene3D | G3DSA:1.20.5.110 | - | 244 | 344 | 1.4E-30 |
| 3 | g13187.t1 | PANTHER | PTHR19957 | SYNTAXIN | 8 | 336 | 3.4E-48 |
| 4 | g13187.t1 | PANTHER | PTHR19957:SF83 | SYNTAXIN-16 | 8 | 336 | 3.4E-48 |
| 1 | g13187.t1 | Pfam | PF00804 | Syntaxin | 225 | 285 | 3.6E-6 |
| 2 | g13187.t1 | Pfam | PF05739 | SNARE domain | 286 | 338 | 3.6E-18 |
| 7 | g13187.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 322 | - |
| 9 | g13187.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 323 | 342 | - |
| 8 | g13187.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 343 | 344 | - |
| 13 | g13187.t1 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 250 | 312 | 18.784 |
| 12 | g13187.t1 | SMART | SM00397 | tSNARE_6 | 245 | 312 | 1.4E-17 |
| 5 | g13187.t1 | SUPERFAMILY | SSF47661 | t-snare proteins | 52 | 305 | 1.65E-32 |
| 11 | g13187.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 323 | 342 | - |
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:0006886 | intracellular protein transport | BP |
| GO:0031201 | SNARE complex | CC |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K08489 (syntaxin 16)
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.
