General information for g11671.t6
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.t6 | TSS | g11671.t6 | 17732807 | 17732807 |
| chr_1 | g11671 | g11671.t6 | isoform | g11671.t6 | 17732842 | 17734025 |
| chr_1 | g11671 | g11671.t6 | exon | g11671.t6.exon1 | 17732842 | 17733776 |
| chr_1 | g11671 | g11671.t6 | cds | g11671.t6.CDS1 | 17733123 | 17733776 |
| chr_1 | g11671 | g11671.t6 | exon | g11671.t6.exon2 | 17733837 | 17734025 |
| chr_1 | g11671 | g11671.t6 | cds | g11671.t6.CDS2 | 17733837 | 17734025 |
| chr_1 | g11671 | g11671.t6 | TTS | g11671.t6 | 17734079 | 17734079 |
Sequences
>g11671.t6 Gene=g11671 Length=1124
ATGGACATTACTGCTTTATTTAAGGCATGTATAAAGTCAGTAAGATTACAGAACAAGCAA
CTTTTAGCATCCGACAAAAATAAAATCTTGAAATCATCAGCAACAAAAGATGAATTGAGT
AAAAAATCAAAGGAAATTCGCTACCAAATTACTCAGTTAAGAAATTTTCTCGTTGAAAAT
AGAGCAGCATATATGCAATTTGCCTGTCATCTCAAAAGATCAGCACAAGTAAGTATCATA
AATAAATATATAATCATAATAATTGCTGATATTTATTTTAGATGACAAATGAAGAGCGAG
ACGTTATTGACAGAGAGGCTGAAAAAATCATAAACATTTGCACACAATTTATCTGTGAAT
TAAAATTAGAATATGGTTCAAGAAACTTGACAAAACAGCAGCGATTACATATAGACGTAG
TTCTTGAGTTGCTTGCTAATTATTTAAAAGCAGTTTATAACATTTTTAATGATCAGAAAA
ATTATAGAATCAGAAGAGATCTTGAAACATATAGATTTCTAAAACTTAACGCTGATCATC
GTCGAGATAATGATAGTATAGACATTAAAAAAATTGAATATAAAGAAAATATGGATCTAA
ATTCAAAAGATGATGATAAAGATAATTTACTTGCAAATGAATTAAAAATGGGAGAAGACG
AAATGATTTTAACACAGAGAAAAAATGCAAAAAATACCAAACGAAATTATGAATCTGAAA
TTATGACTGCAAGTAATCAATCAATGTCAATGGAAGATGATGTAAATTCCAATCAAAATG
ATGCTACTTTTGGGTTAAGTGCTGAAGACTTACAAATGTTAGAGATTGAAAACAAGCAAA
TGTTAACTCAATTTCAAGGGCTTAATGAAGAGGTTCAACAAATTGAAAAACATGTCTATG
ATATAGCAAAACTACAAGAAATTTTCACTGAAAAAGTTGTATTACAAAAAGCAGATATTG
AACGTATTTCAAATTCAGTTGTTGGTGCTACTGAGAATGTTCGTGAAGCAAATGAACAGA
TAAGAGAGGCAATACAAAGAAATGCTGGTTTAAGAGTTTACGTTCTATTCTTTCTTCTTG
TCATGTCATTTTCCTTACTATTTTTAGACTGGTACAATGACTGA
>g11671.t6 Gene=g11671 Length=280
MTNEERDVIDREAEKIINICTQFICELKLEYGSRNLTKQQRLHIDVVLELLANYLKAVYN
IFNDQKNYRIRRDLETYRFLKLNADHRRDNDSIDIKKIEYKENMDLNSKDDDKDNLLANE
LKMGEDEMILTQRKNAKNTKRNYESEIMTASNQSMSMEDDVNSNQNDATFGLSAEDLQML
EIENKQMLTQFQGLNEEVQQIEKHVYDIAKLQEIFTEKVVLQKADIERISNSVVGATENV
REANEQIREAIQRNAGLRVYVLFFLLVMSFSLLFLDWYND
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11671.t6 | Coils | Coil | Coil | 133 | 153 | - |
| 5 | g11671.t6 | Coils | Coil | Coil | 177 | 204 | - |
| 6 | g11671.t6 | Coils | Coil | Coil | 226 | 253 | - |
| 4 | g11671.t6 | Gene3D | G3DSA:1.20.5.110 | - | 178 | 276 | 1.3E-5 |
| 1 | g11671.t6 | PANTHER | PTHR15959 | SYNTAXIN-18 | 1 | 279 | 2.4E-52 |
| 8 | g11671.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 256 | - |
| 10 | g11671.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 257 | 278 | - |
| 9 | g11671.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 279 | 280 | - |
| 3 | g11671.t6 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 186 | 252 | 6.34E-7 |
| 2 | g11671.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 256 | 278 | - |
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.
