General information for g7559.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Syntaxin-6.
Parent gene
- The parent gene g7559 is located on chr_2: 24523018..24524312 (- 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_2 | g7559 | g7559.t1 | TTS | g7559.t1 | 24522902 | 24522902 |
| chr_2 | g7559 | g7559.t1 | isoform | g7559.t1 | 24523018 | 24524312 |
| chr_2 | g7559 | g7559.t1 | exon | g7559.t1.exon1 | 24523018 | 24523192 |
| chr_2 | g7559 | g7559.t1 | cds | g7559.t1.CDS1 | 24523018 | 24523192 |
| chr_2 | g7559 | g7559.t1 | exon | g7559.t1.exon2 | 24523253 | 24523906 |
| chr_2 | g7559 | g7559.t1 | cds | g7559.t1.CDS2 | 24523253 | 24523906 |
| chr_2 | g7559 | g7559.t1 | exon | g7559.t1.exon3 | 24524275 | 24524312 |
| chr_2 | g7559 | g7559.t1 | cds | g7559.t1.CDS3 | 24524275 | 24524312 |
| chr_2 | g7559 | g7559.t1 | TSS | g7559.t1 | 24524278 | 24524278 |
Sequences
>g7559.t1 Gene=g7559 Length=867
ATGGGTAAAATTATGTTGGATATTTCACGCATGCACCGTGAAGTTTTTAAAGGACTAAAT
AAAACTCGTGGGCTCTTTTTGCGATATCGCGAACTTCAAAACGATACGAGTGCAAGTGAT
CAACAAACGGACCTTGAGTATACAACTACTGAATTGAGAAACTCATTGAGATCAATTGAA
TGGGATCTTGAAGATTTAGAAGATACAATTGCAATAGCTGAGAAAAATCCAAAACATAAA
ATCGACTTACAGGAACTAAATCAGCGAAGGAATTTCATAATTGCCACAAAAAATGAGATC
AAGTCTATGAAAGATAAAATTAGTATTTTAAAGAATCGTGATAAAGATATAACTGCGATT
CAGCCACTACTTGACGACGATCCTTCACCAAAGAACACTTCAAACAGTAATTGCAACGGT
AATACATCAAATTCTATTGGGAATAATTTAATGAGCAGTATGGCAGCAGCAAGACACAGC
GGTACTAAATATAAGAAACTCGAAAACATCAACGACAGTCCCAGTCATAATGGAAACTTT
AACAGTGACAGTGCTTTTATGGGCGAAACAATTTCAATTCAACAGAGAATGCTACAATCT
CAAGATTTACAAATCGATGTTTTGAGCGATTCAATAGGCACATTAAAAACCGTTAGTCGA
CAAATTGGTGTAGAAATTGATGAGCAAGCTGTTATGCTAGATGAATTTGGTAATGAATTA
GATGCCACAGACTCAAAATTGGATGCTACAATGAAGAAAGTTGGAAAAGTGCTTCATTTA
TCAGGCAACGATAGACGTCAATGGATGGCAATTGGATTTCTGAGCATCCTTTTAATAGTT
GTGATAATTCTTTTCATAATTCTTTAA
>g7559.t1 Gene=g7559 Length=288
MGKIMLDISRMHREVFKGLNKTRGLFLRYRELQNDTSASDQQTDLEYTTTELRNSLRSIE
WDLEDLEDTIAIAEKNPKHKIDLQELNQRRNFIIATKNEIKSMKDKISILKNRDKDITAI
QPLLDDDPSPKNTSNSNCNGNTSNSIGNNLMSSMAAARHSGTKYKKLENINDSPSHNGNF
NSDSAFMGETISIQQRMLQSQDLQIDVLSDSIGTLKTVSRQIGVEIDEQAVMLDEFGNEL
DATDSKLDATMKKVGKVLHLSGNDRRQWMAIGFLSILLIVVIILFIIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g7559.t1 | CDD | cd15851 | SNARE_Syntaxin6 | 198 | 261 | 7.31775E-21 |
| 11 | g7559.t1 | Coils | Coil | Coil | 49 | 76 | - |
| 10 | g7559.t1 | Coils | Coil | Coil | 93 | 113 | - |
| 9 | g7559.t1 | Gene3D | G3DSA:1.20.58.90 | - | 9 | 109 | 4.7E-31 |
| 8 | g7559.t1 | Gene3D | G3DSA:1.20.5.110 | - | 202 | 267 | 2.7E-23 |
| 18 | g7559.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 120 | 141 | - |
| 19 | g7559.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 127 | 141 | - |
| 2 | g7559.t1 | PANTHER | PTHR19957 | SYNTAXIN | 10 | 109 | 4.3E-40 |
| 4 | g7559.t1 | PANTHER | PTHR19957:SF104 | SYNTAXIN-6 | 10 | 109 | 4.3E-40 |
| 3 | g7559.t1 | PANTHER | PTHR19957 | SYNTAXIN | 181 | 288 | 4.3E-40 |
| 5 | g7559.t1 | PANTHER | PTHR19957:SF104 | SYNTAXIN-6 | 181 | 288 | 4.3E-40 |
| 1 | g7559.t1 | Pfam | PF09177 | Syntaxin 6, N-terminal | 11 | 104 | 1.0E-25 |
| 12 | g7559.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 267 | - |
| 14 | g7559.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 268 | 287 | - |
| 13 | g7559.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 288 | 288 | - |
| 20 | g7559.t1 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 195 | 257 | 15.084 |
| 17 | g7559.t1 | SMART | SM00397 | tSNARE_6 | 190 | 257 | 1.7E-7 |
| 7 | g7559.t1 | SUPERFAMILY | SSF47661 | t-snare proteins | 12 | 107 | 1.49E-19 |
| 6 | g7559.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 190 | 258 | 2.44E-15 |
| 16 | g7559.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 268 | 287 | - |
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:0048193 | Golgi vesicle transport | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K08498 (syntaxin 6)
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.
