General information for g959.t11
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.t11 | TSS | g959.t11 | 7041748 | 7041748 |
| chr_3 | g959 | g959.t11 | isoform | g959.t11 | 7042263 | 7060460 |
| chr_3 | g959 | g959.t11 | exon | g959.t11.exon1 | 7042263 | 7042295 |
| chr_3 | g959 | g959.t11 | exon | g959.t11.exon2 | 7051815 | 7051995 |
| chr_3 | g959 | g959.t11 | exon | g959.t11.exon3 | 7052074 | 7052136 |
| chr_3 | g959 | g959.t11 | exon | g959.t11.exon4 | 7052347 | 7052530 |
| chr_3 | g959 | g959.t11 | cds | g959.t11.CDS1 | 7052455 | 7052530 |
| chr_3 | g959 | g959.t11 | exon | g959.t11.exon5 | 7052601 | 7052674 |
| chr_3 | g959 | g959.t11 | cds | g959.t11.CDS2 | 7052601 | 7052674 |
| chr_3 | g959 | g959.t11 | exon | g959.t11.exon6 | 7052753 | 7052890 |
| chr_3 | g959 | g959.t11 | cds | g959.t11.CDS3 | 7052753 | 7052890 |
| chr_3 | g959 | g959.t11 | exon | g959.t11.exon7 | 7054214 | 7054324 |
| chr_3 | g959 | g959.t11 | cds | g959.t11.CDS4 | 7054214 | 7054324 |
| chr_3 | g959 | g959.t11 | exon | g959.t11.exon8 | 7060239 | 7060460 |
| chr_3 | g959 | g959.t11 | cds | g959.t11.CDS5 | 7060239 | 7060316 |
| chr_3 | g959 | g959.t11 | TTS | g959.t11 | 7060535 | 7060535 |
Sequences
>g959.t11 Gene=g959 Length=1006
ATGACGAAGGATAGATTAGCAGCATTGCATGCGGCTCAAAGTGATGACGAGGATGCGGGG
ATGGATGAAGTTGCCATCAACGTCGATGGCTTCATGGAGGAGTTTTTCACTGAGGTGGAA
GAAGTTAGAGAGATGATAGATAAAATACAATATAATGTGGAAGAGGTTAAGAAAAAACAC
AGTTCCATCTTATCCGCTCCTCAAACGGATGAAAAAACCAAGCAAGAGTTAGAGGATCTG
ATGGCAGATATTAAGAAAAATGCCAATAGGTATACTAAATATCGAACAAAGTATCGAGCA
AGAAGAGCAGAGTAAATCAGCAAGTGCCGATTTACGAATACGTAAGACACAACATTCGAC
ATTATCACGAAAATTTGTCGAAGTAATGACAGAATATAATCGAACACAAACTGATTATCG
AGAGAGATGTAAAGCGAGAATACAACGTCAATTGGAAATCACTGGTAAAGCCACAACAAA
TGAAGAACTCGAAGAAATGTTGGAGCAAGGAAATTCGGCAGTGTTTACACAAGGAATTAT
TATGGAAACACAACAAGCAAAACAGACCCTGGCAGATATCGAAGCACGACATGCTGATAT
CATTAAACTTGAAAACTCAATTCGAGAATTGCACGATATGTTCATGGATATGGCAATGTT
GGTCGAGAGTCAGGGAGAATTGGTGGATCGGATTGAGAACCATGTTGAGGAGGGCAAGGA
TTTCACTGAAAATGCAAAGAAGCAAATTTATCAGGCTTCCGTGTATGCGAAAAAGGCGAG
GAAGAAAAAAATTTATATCATAATCTGCCTGACGATAGTAGGAATTCTATTGCTATTGTA
TCTATACAGTCTCATCTTTTGATTGGAATAACTGCCACTTCAGCAAAAAACACAACGACT
ATTTATGATGTCATCTATCTAATCTATATAATTTTTTGTTCTACAAGTTGTCATTATACT
TTTATATGTATATTTGTCATCGAAGTATCCTTTTTATTGCATTGTT
>g959.t11 Gene=g959 Length=158
MTEYNRTQTDYRERCKARIQRQLEITGKATTNEELEEMLEQGNSAVFTQGIIMETQQAKQ
TLADIEARHADIIKLENSIRELHDMFMDMAMLVESQGELVDRIENHVEEGKDFTENAKKQ
IYQASVYAKKARKKKIYIIICLTIVGILLLLYLYSLIF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g959.t11 | Gene3D | G3DSA:1.20.58.70 | - | 1 | 117 | 5.6E-52 |
| 3 | g959.t11 | PANTHER | PTHR19957:SF231 | SYNTAXIN-1A HOMOLOG | 1 | 152 | 4.5E-66 |
| 4 | g959.t11 | PANTHER | PTHR19957 | SYNTAXIN | 1 | 152 | 4.5E-66 |
| 1 | g959.t11 | Pfam | PF00804 | Syntaxin | 1 | 97 | 1.5E-37 |
| 2 | g959.t11 | Pfam | PF05739 | SNARE domain | 98 | 150 | 1.5E-14 |
| 7 | g959.t11 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 135 | - |
| 9 | g959.t11 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 157 | - |
| 8 | g959.t11 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 158 | 158 | - |
| 11 | g959.t11 | ProSitePatterns | PS00914 | Syntaxin / epimorphin family signature. | 68 | 107 | - |
| 13 | g959.t11 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 62 | 124 | 18.321 |
| 12 | g959.t11 | SMART | SM00397 | tSNARE_6 | 57 | 124 | 7.2E-19 |
| 5 | g959.t11 | SUPERFAMILY | SSF47661 | t-snare proteins | 1 | 117 | 3.18E-39 |
| 10 | g959.t11 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 157 | - |
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: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.
