General information for g11671.t2
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.t2 | isoform | g11671.t2 | 17729643 | 17734025 |
| chr_1 | g11671 | g11671.t2 | exon | g11671.t2.exon1 | 17729643 | 17729754 |
| chr_1 | g11671 | g11671.t2 | exon | g11671.t2.exon2 | 17732820 | 17733069 |
| chr_1 | g11671 | g11671.t2 | cds | g11671.t2.CDS1 | 17732842 | 17733069 |
| chr_1 | g11671 | g11671.t2 | exon | g11671.t2.exon3 | 17733123 | 17733780 |
| chr_1 | g11671 | g11671.t2 | cds | g11671.t2.CDS2 | 17733123 | 17733780 |
| chr_1 | g11671 | g11671.t2 | exon | g11671.t2.exon4 | 17733851 | 17734025 |
| chr_1 | g11671 | g11671.t2 | cds | g11671.t2.CDS3 | 17733851 | 17733924 |
| chr_1 | g11671 | g11671.t2 | TTS | g11671.t2 | 17734079 | 17734079 |
| chr_1 | g11671 | g11671.t2 | TSS | g11671.t2 | NA | NA |
Sequences
>g11671.t2 Gene=g11671 Length=1195
CTCTTTTTGTTTCTGCTCGATTTTTCATTTGAAATAGTATAAACATCATCATGCTGTCGT
CTTTTGTTGCTTTTAAATCTTTGTTTTTCACCATAATAGTTTTGTTTTCTTTTAATTTTT
TGTTTTTGAACAAAATGGACATTACTGCTTTATTTAAGGCATGTATAAAGTCAGTAAGAT
TACAGAACAAGCAACTTTTAGCATCCGACAAAAATAAAATCTTGAAATCATCAGCAACAA
AAGATGAATTGAGTAAAAAATCAAAGGAAATTCGCTACCAAATTACTCAGTTAAGAAATT
TTCTCGTTGAAAATAGAGCAGCATATATGCAATTTGCCTGTCATCTCAAAAGATCAGCAC
AAATGACAAATGAAGAGCGAGACGTTATTGACAGAGAGGCTGAAAAAATCATAAACATTT
GCACACAATTTATCTGTGAATTAAAATTAGAATATGGTTCAAGAAACTTGACAAAACAGC
AGCGATTACATATAGACGTAGTTCTTGAGTTGCTTGCTAATTATTTAAAAGCAGTTTATA
ACATTTTTAATGATCAGAAAAATTATAGAATCAGAAGAGATCTTGAAACATATAGATTTC
TAAAACTTAACGCTGATCATCGTCGAGATAATGATAGTATAGACATTAAAAAAATTGAAT
ATAAAGAAAATATGGATCTAAATTCAAAAGATGATGATAAAGATAATTTACTTGCAAATG
AATTAAAAATGGGAGAAGACGAAATGATTTTAACACAGAGAAAAAATGCAAAAAATACCA
AACGAAATTATGAATCTGAAATTATGACTGCAAGTAATCAATCAATGTCAATGGAAGATG
ATGTAAATTCCAATCAAAATGATGCTACTTTTGGGTTAAGTGCTGAAGACTTACAAATGT
TAGAGATTGAAAACAAGCAAATGTTAACTCAATTTCAAGGGCTTAATGAAGAGGTTCAAC
AAATTGAAAAACATGTCTATGATATAGCAAAACTACAAGAAATTTTCACTGAAAAAGTTA
AGCAGATATTGAACGTATTTCAAATTCAGTTGTTGGTGCTACTGAGAATGTTCGTGAAGC
AAATGAACAGATAAGAGAGGCAATACAAAGAAATGCTGGTTTAAGAGTTTACGTTCTATT
CTTTCTTCTTGTCATGTCATTTTCCTTACTATTTTTAGACTGGTACAATGACTGA
>g11671.t2 Gene=g11671 Length=319
MDITALFKACIKSVRLQNKQLLASDKNKILKSSATKDELSKKSKEIRYQITQLRNFLVEN
RAAYMQFACHLKRSAQMTNEERDVIDREAEKIINICTQFICELKLEYGSRNLTKQQRLHI
DVVLELLANYLKAVYNIFNDQKNYRIRRDLETYRFLKLNADHRRDNDSIDIKKIEYKENM
DLNSKDDDKDNLLANELKMGEDEMILTQRKNAKNTKRNYESEIMTASNQSMSMEDDVNSN
QNDATFGLSAEDLQMLEIENKQMLTQFQGLNEEVQQIEKHVYDIAKLQEIFTEKVKQILN
VFQIQLLVLLRMFVKQMNR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11671.t2 | Coils | Coil | Coil | 209 | 229 | - |
| 4 | g11671.t2 | Coils | Coil | Coil | 253 | 280 | - |
| 2 | g11671.t2 | PANTHER | PTHR15959:SF0 | SYNTAXIN-18 | 1 | 297 | 1.0E-37 |
| 3 | g11671.t2 | PANTHER | PTHR15959 | SYNTAXIN-18 | 1 | 297 | 1.0E-37 |
| 1 | g11671.t2 | Pfam | PF10496 | SNARE-complex protein Syntaxin-18 N-terminus | 1 | 84 | 1.0E-18 |
| 7 | g11671.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 296 | - |
| 8 | g11671.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 297 | 314 | - |
| 6 | g11671.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 315 | 319 | - |
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.
