General information for g959.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t10 | TSS | g959.t10 | 7041748 | 7041748 |
| chr_3 | g959 | g959.t10 | isoform | g959.t10 | 7042263 | 7052529 |
| chr_3 | g959 | g959.t10 | exon | g959.t10.exon1 | 7042263 | 7042295 |
| chr_3 | g959 | g959.t10 | cds | g959.t10.CDS1 | 7042263 | 7042295 |
| chr_3 | g959 | g959.t10 | exon | g959.t10.exon2 | 7051815 | 7051995 |
| chr_3 | g959 | g959.t10 | cds | g959.t10.CDS2 | 7051815 | 7051995 |
| chr_3 | g959 | g959.t10 | exon | g959.t10.exon3 | 7052074 | 7052128 |
| chr_3 | g959 | g959.t10 | cds | g959.t10.CDS3 | 7052074 | 7052128 |
| chr_3 | g959 | g959.t10 | exon | g959.t10.exon4 | 7052347 | 7052529 |
| chr_3 | g959 | g959.t10 | cds | g959.t10.CDS4 | 7052347 | 7052455 |
| chr_3 | g959 | g959.t10 | TTS | g959.t10 | NA | NA |
Sequences
>g959.t10 Gene=g959 Length=452
ATGACGAAGGATAGATTAGCAGCATTGCATGCGGCTCAAAGTGATGACGAGGATGCGGGG
ATGGATGAAGTTGCCATCAACGTCGATGGCTTCATGGAGGAGTTTTTCACTGAGGTGGAA
GAAGTTAGAGAGATGATAGATAAAATACAATATAATGTGGAAGAGGTTAAGAAAAAACAC
AGTTCCATCTTATCCGCTCCTCAAACGGATGAAAAAACCAAGCAAGAGTTAGAGGATCTG
ATGGCAGATATTAAGAAAAATGCCAATAGAATATCGAACAAAGTATCGAGCAAGAAGAGC
AGAGTAAATCAGCAAGTGCCGATTTACGAATACGTAAGACACAACATTCGACATTATCAC
GAAAATTTGTCGAAGTAATGACAGAATATAATCGAACACAAACTGATTATCGAGAGAGAT
GTAAAGCGAGAATACAACGTCAATTGGAAATC
>g959.t10 Gene=g959 Length=125
MTKDRLAALHAAQSDDEDAGMDEVAINVDGFMEEFFTEVEEVREMIDKIQYNVEEVKKKH
SSILSAPQTDEKTKQELEDLMADIKKNANRISNKVSSKKSRVNQQVPIYEYVRHNIRHYH
ENLSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g959.t10 | Coils | Coil | Coil | 39 | 59 | - |
| 9 | g959.t10 | Coils | Coil | Coil | 74 | 94 | - |
| 8 | g959.t10 | Gene3D | G3DSA:1.20.58.70 | - | 31 | 124 | 4.3E-24 |
| 6 | g959.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 7 | g959.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 17 | - |
| 2 | g959.t10 | PANTHER | PTHR19957:SF84 | SYNTAXIN-1A | 20 | 105 | 3.5E-27 |
| 3 | g959.t10 | PANTHER | PTHR19957 | SYNTAXIN | 20 | 105 | 3.5E-27 |
| 1 | g959.t10 | Pfam | PF00804 | Syntaxin | 32 | 99 | 1.4E-10 |
| 5 | g959.t10 | SMART | SM00503 | SynN_4 | 27 | 124 | 4.0E-4 |
| 4 | g959.t10 | SUPERFAMILY | SSF47661 | t-snare proteins | 31 | 100 | 1.02E-18 |
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: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 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. There were no conditions that were differentially expressed