General information for g11671.t4
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.t4 | TSS | g11671.t4 | 17732807 | 17732807 |
| chr_1 | g11671 | g11671.t4 | isoform | g11671.t4 | 17732842 | 17734025 |
| chr_1 | g11671 | g11671.t4 | exon | g11671.t4.exon1 | 17732842 | 17733069 |
| chr_1 | g11671 | g11671.t4 | cds | g11671.t4.CDS1 | 17732842 | 17733069 |
| chr_1 | g11671 | g11671.t4 | exon | g11671.t4.exon2 | 17733123 | 17733780 |
| chr_1 | g11671 | g11671.t4 | cds | g11671.t4.CDS2 | 17733123 | 17733780 |
| chr_1 | g11671 | g11671.t4 | exon | g11671.t4.exon3 | 17733837 | 17734025 |
| chr_1 | g11671 | g11671.t4 | cds | g11671.t4.CDS3 | 17733837 | 17733862 |
| chr_1 | g11671 | g11671.t4 | TTS | g11671.t4 | 17734079 | 17734079 |
Sequences
>g11671.t4 Gene=g11671 Length=1075
ATGGACATTACTGCTTTATTTAAGGCATGTATAAAGTCAGTAAGATTACAGAACAAGCAA
CTTTTAGCATCCGACAAAAATAAAATCTTGAAATCATCAGCAACAAAAGATGAATTGAGT
AAAAAATCAAAGGAAATTCGCTACCAAATTACTCAGTTAAGAAATTTTCTCGTTGAAAAT
AGAGCAGCATATATGCAATTTGCCTGTCATCTCAAAAGATCAGCACAAATGACAAATGAA
GAGCGAGACGTTATTGACAGAGAGGCTGAAAAAATCATAAACATTTGCACACAATTTATC
TGTGAATTAAAATTAGAATATGGTTCAAGAAACTTGACAAAACAGCAGCGATTACATATA
GACGTAGTTCTTGAGTTGCTTGCTAATTATTTAAAAGCAGTTTATAACATTTTTAATGAT
CAGAAAAATTATAGAATCAGAAGAGATCTTGAAACATATAGATTTCTAAAACTTAACGCT
GATCATCGTCGAGATAATGATAGTATAGACATTAAAAAAATTGAATATAAAGAAAATATG
GATCTAAATTCAAAAGATGATGATAAAGATAATTTACTTGCAAATGAATTAAAAATGGGA
GAAGACGAAATGATTTTAACACAGAGAAAAAATGCAAAAAATACCAAACGAAATTATGAA
TCTGAAATTATGACTGCAAGTAATCAATCAATGTCAATGGAAGATGATGTAAATTCCAAT
CAAAATGATGCTACTTTTGGGTTAAGTGCTGAAGACTTACAAATGTTAGAGATTGAAAAC
AAGCAAATGTTAACTCAATTTCAAGGGCTTAATGAAGAGGTTCAACAAATTGAAAAACAT
GTCTATGATATAGCAAAACTACAAGAAATTTTCACTGAAAAAGTTAGTTGTATTACAAAA
AGCAGATATTGAACGTATTTCAAATTCAGTTGTTGGTGCTACTGAGAATGTTCGTGAAGC
AAATGAACAGATAAGAGAGGCAATACAAAGAAATGCTGGTTTAAGAGTTTACGTTCTATT
CTTTCTTCTTGTCATGTCATTTTCCTTACTATTTTTAGACTGGTACAATGACTGA
>g11671.t4 Gene=g11671 Length=303
MDITALFKACIKSVRLQNKQLLASDKNKILKSSATKDELSKKSKEIRYQITQLRNFLVEN
RAAYMQFACHLKRSAQMTNEERDVIDREAEKIINICTQFICELKLEYGSRNLTKQQRLHI
DVVLELLANYLKAVYNIFNDQKNYRIRRDLETYRFLKLNADHRRDNDSIDIKKIEYKENM
DLNSKDDDKDNLLANELKMGEDEMILTQRKNAKNTKRNYESEIMTASNQSMSMEDDVNSN
QNDATFGLSAEDLQMLEIENKQMLTQFQGLNEEVQQIEKHVYDIAKLQEIFTEKVSCITK
SRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11671.t4 | Coils | Coil | Coil | 209 | 229 | - |
| 4 | g11671.t4 | Coils | Coil | Coil | 253 | 280 | - |
| 2 | g11671.t4 | PANTHER | PTHR15959:SF0 | SYNTAXIN-18 | 1 | 295 | 1.3E-37 |
| 3 | g11671.t4 | PANTHER | PTHR15959 | SYNTAXIN-18 | 1 | 295 | 1.3E-37 |
| 1 | g11671.t4 | Pfam | PF10496 | SNARE-complex protein Syntaxin-18 N-terminus | 1 | 84 | 9.4E-19 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
