General information for g11671.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Syntaxin-18.
Parent gene
- The parent gene g11671 is located on chr_1: 17734025..17737163 (+ 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 | g11671 | g11671.t1 | TSS | g11671.t1 | 17732807 | 17732807 |
| chr_1 | g11671 | g11671.t1 | isoform | g11671.t1 | 17732842 | 17734025 |
| chr_1 | g11671 | g11671.t1 | exon | g11671.t1.exon1 | 17732842 | 17733069 |
| chr_1 | g11671 | g11671.t1 | cds | g11671.t1.CDS1 | 17732842 | 17733069 |
| chr_1 | g11671 | g11671.t1 | exon | g11671.t1.exon2 | 17733123 | 17733776 |
| chr_1 | g11671 | g11671.t1 | cds | g11671.t1.CDS2 | 17733123 | 17733776 |
| chr_1 | g11671 | g11671.t1 | exon | g11671.t1.exon3 | 17733837 | 17734025 |
| chr_1 | g11671 | g11671.t1 | cds | g11671.t1.CDS3 | 17733837 | 17734025 |
| chr_1 | g11671 | g11671.t1 | TTS | g11671.t1 | 17734079 | 17734079 |
Sequences
>g11671.t1 Gene=g11671 Length=1071
ATGGACATTACTGCTTTATTTAAGGCATGTATAAAGTCAGTAAGATTACAGAACAAGCAA
CTTTTAGCATCCGACAAAAATAAAATCTTGAAATCATCAGCAACAAAAGATGAATTGAGT
AAAAAATCAAAGGAAATTCGCTACCAAATTACTCAGTTAAGAAATTTTCTCGTTGAAAAT
AGAGCAGCATATATGCAATTTGCCTGTCATCTCAAAAGATCAGCACAAATGACAAATGAA
GAGCGAGACGTTATTGACAGAGAGGCTGAAAAAATCATAAACATTTGCACACAATTTATC
TGTGAATTAAAATTAGAATATGGTTCAAGAAACTTGACAAAACAGCAGCGATTACATATA
GACGTAGTTCTTGAGTTGCTTGCTAATTATTTAAAAGCAGTTTATAACATTTTTAATGAT
CAGAAAAATTATAGAATCAGAAGAGATCTTGAAACATATAGATTTCTAAAACTTAACGCT
GATCATCGTCGAGATAATGATAGTATAGACATTAAAAAAATTGAATATAAAGAAAATATG
GATCTAAATTCAAAAGATGATGATAAAGATAATTTACTTGCAAATGAATTAAAAATGGGA
GAAGACGAAATGATTTTAACACAGAGAAAAAATGCAAAAAATACCAAACGAAATTATGAA
TCTGAAATTATGACTGCAAGTAATCAATCAATGTCAATGGAAGATGATGTAAATTCCAAT
CAAAATGATGCTACTTTTGGGTTAAGTGCTGAAGACTTACAAATGTTAGAGATTGAAAAC
AAGCAAATGTTAACTCAATTTCAAGGGCTTAATGAAGAGGTTCAACAAATTGAAAAACAT
GTCTATGATATAGCAAAACTACAAGAAATTTTCACTGAAAAAGTTGTATTACAAAAAGCA
GATATTGAACGTATTTCAAATTCAGTTGTTGGTGCTACTGAGAATGTTCGTGAAGCAAAT
GAACAGATAAGAGAGGCAATACAAAGAAATGCTGGTTTAAGAGTTTACGTTCTATTCTTT
CTTCTTGTCATGTCATTTTCCTTACTATTTTTAGACTGGTACAATGACTGA
>g11671.t1 Gene=g11671 Length=356
MDITALFKACIKSVRLQNKQLLASDKNKILKSSATKDELSKKSKEIRYQITQLRNFLVEN
RAAYMQFACHLKRSAQMTNEERDVIDREAEKIINICTQFICELKLEYGSRNLTKQQRLHI
DVVLELLANYLKAVYNIFNDQKNYRIRRDLETYRFLKLNADHRRDNDSIDIKKIEYKENM
DLNSKDDDKDNLLANELKMGEDEMILTQRKNAKNTKRNYESEIMTASNQSMSMEDDVNSN
QNDATFGLSAEDLQMLEIENKQMLTQFQGLNEEVQQIEKHVYDIAKLQEIFTEKVVLQKA
DIERISNSVVGATENVREANEQIREAIQRNAGLRVYVLFFLLVMSFSLLFLDWYND
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11671.t1 | Coils | Coil | Coil | 209 | 229 | - |
| 7 | g11671.t1 | Coils | Coil | Coil | 253 | 280 | - |
| 9 | g11671.t1 | Coils | Coil | Coil | 302 | 329 | - |
| 6 | g11671.t1 | Gene3D | G3DSA:1.20.5.110 | - | 254 | 352 | 2.0E-5 |
| 2 | g11671.t1 | PANTHER | PTHR15959:SF0 | SYNTAXIN-18 | 1 | 355 | 1.3E-68 |
| 3 | g11671.t1 | PANTHER | PTHR15959 | SYNTAXIN-18 | 1 | 355 | 1.3E-68 |
| 1 | g11671.t1 | Pfam | PF10496 | SNARE-complex protein Syntaxin-18 N-terminus | 1 | 84 | 1.3E-18 |
| 10 | g11671.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 332 | - |
| 12 | g11671.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 333 | 354 | - |
| 11 | g11671.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 355 | 356 | - |
| 5 | g11671.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 262 | 328 | 9.81E-7 |
| 4 | g11671.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 332 | 354 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K08492 (syntaxin 18)
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.
