General information for g959.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Syntaxin-1A.
Parent gene
- The parent gene g959 is located on chr_3: 7052529..7062065 (+ 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_3 | g959 | g959.t1 | TSS | g959.t1 | 7041748 | 7041748 |
| chr_3 | g959 | g959.t1 | isoform | g959.t1 | 7042263 | 7053237 |
| chr_3 | g959 | g959.t1 | exon | g959.t1.exon1 | 7042263 | 7042295 |
| chr_3 | g959 | g959.t1 | cds | g959.t1.CDS1 | 7042263 | 7042295 |
| chr_3 | g959 | g959.t1 | exon | g959.t1.exon2 | 7051815 | 7051995 |
| chr_3 | g959 | g959.t1 | cds | g959.t1.CDS2 | 7051815 | 7051995 |
| chr_3 | g959 | g959.t1 | exon | g959.t1.exon3 | 7052074 | 7052128 |
| chr_3 | g959 | g959.t1 | cds | g959.t1.CDS3 | 7052074 | 7052128 |
| chr_3 | g959 | g959.t1 | exon | g959.t1.exon4 | 7052231 | 7052249 |
| chr_3 | g959 | g959.t1 | cds | g959.t1.CDS4 | 7052231 | 7052249 |
| chr_3 | g959 | g959.t1 | exon | g959.t1.exon5 | 7052347 | 7052530 |
| chr_3 | g959 | g959.t1 | cds | g959.t1.CDS5 | 7052347 | 7052530 |
| chr_3 | g959 | g959.t1 | exon | g959.t1.exon6 | 7052601 | 7052674 |
| chr_3 | g959 | g959.t1 | cds | g959.t1.CDS6 | 7052601 | 7052674 |
| chr_3 | g959 | g959.t1 | exon | g959.t1.exon7 | 7052753 | 7052890 |
| chr_3 | g959 | g959.t1 | cds | g959.t1.CDS7 | 7052753 | 7052890 |
| chr_3 | g959 | g959.t1 | exon | g959.t1.exon8 | 7053118 | 7053237 |
| chr_3 | g959 | g959.t1 | cds | g959.t1.CDS8 | 7053118 | 7053237 |
| chr_3 | g959 | g959.t1 | TTS | g959.t1 | NA | NA |
Sequences
>g959.t1 Gene=g959 Length=804
ATGACGAAGGATAGATTAGCAGCATTGCATGCGGCTCAAAGTGATGACGAGGATGCGGGG
ATGGATGAAGTTGCCATCAACGTCGATGGCTTCATGGAGGAGTTTTTCACTGAGGTGGAA
GAAGTTAGAGAGATGATAGATAAAATACAATATAATGTGGAAGAGGTTAAGAAAAAACAC
AGTTCCATCTTATCCGCTCCTCAAACGGATGAAAAAACCAAGCAAGAGTTAGAGGATCTG
ATGGCAGATATTAAGAAAAATGCCAATAGAGTTAGAGGAAAACTAAAGAATATCGAACAA
AGTATCGAGCAAGAAGAGCAGAGTAAATCAGCAAGTGCCGATTTACGAATACGTAAGACA
CAACATTCGACATTATCACGAAAATTTGTCGAAGTAATGACAGAATATAATCGAACACAA
ACTGATTATCGAGAGAGATGTAAAGCGAGAATACAACGTCAATTGGAAATCACTGGTAAA
GCCACAACAAATGAAGAACTCGAAGAAATGTTGGAGCAAGGAAATTCGGCAGTGTTTACA
CAAGGAATTATTATGGAAACACAACAAGCAAAACAGACCCTGGCAGATATCGAAGCACGA
CATGCTGATATCATTAAACTTGAAAACTCAATTCGAGAATTGCACGATATGTTCATGGAT
ATGGCAATGTTGGTCGAGAGTCAGGGTGAAATGATTGATCGTATAGAGTATCATGTTGAG
CATGCAATGGATTATGTCCAAACAGCTACACAAGATACCAAAAAAGCACTCAAATACCAA
AGTAAAGCTCGTCGGGTAAGTTGA
>g959.t1 Gene=g959 Length=267
MTKDRLAALHAAQSDDEDAGMDEVAINVDGFMEEFFTEVEEVREMIDKIQYNVEEVKKKH
SSILSAPQTDEKTKQELEDLMADIKKNANRVRGKLKNIEQSIEQEEQSKSASADLRIRKT
QHSTLSRKFVEVMTEYNRTQTDYRERCKARIQRQLEITGKATTNEELEEMLEQGNSAVFT
QGIIMETQQAKQTLADIEARHADIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYHVE
HAMDYVQTATQDTKKALKYQSKARRVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g959.t1 | CDD | cd00179 | SynN | 43 | 183 | 7.63111E-50 |
| 10 | g959.t1 | CDD | cd15880 | SNARE_syntaxin1 | 193 | 261 | 3.43899E-36 |
| 8 | g959.t1 | Coils | Coil | Coil | 39 | 59 | - |
| 7 | g959.t1 | Coils | Coil | Coil | 74 | 108 | - |
| 6 | g959.t1 | Gene3D | G3DSA:1.20.58.70 | - | 26 | 249 | 2.8E-96 |
| 3 | g959.t1 | PANTHER | PTHR19957:SF84 | SYNTAXIN-1A | 20 | 266 | 1.3E-120 |
| 4 | g959.t1 | PANTHER | PTHR19957 | SYNTAXIN | 20 | 266 | 1.3E-120 |
| 1 | g959.t1 | Pfam | PF00804 | Syntaxin | 32 | 229 | 1.3E-62 |
| 2 | g959.t1 | Pfam | PF05739 | SNARE domain | 230 | 265 | 8.6E-12 |
| 11 | g959.t1 | ProSitePatterns | PS00914 | Syntaxin / epimorphin family signature. | 200 | 239 | - |
| 14 | g959.t1 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 194 | 256 | 20.749 |
| 12 | g959.t1 | SMART | SM00503 | SynN_4 | 27 | 148 | 1.9E-39 |
| 13 | g959.t1 | SMART | SM00397 | tSNARE_6 | 189 | 256 | 4.3E-21 |
| 5 | g959.t1 | SUPERFAMILY | SSF47661 | t-snare proteins | 30 | 249 | 4.71E-67 |
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:0006886 | intracellular protein transport | BP |
| GO:0005484 | SNAP receptor activity | MF |
| GO:0000149 | SNARE binding | MF |
| GO:0017157 | regulation of exocytosis | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K04560 (syntaxin 1A)
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.
