General information for g9272.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Syntaxin-4.
Parent gene
- The parent gene g9272 is located on chr_1: 1385908..1387224 (+ 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 | g9272 | g9272.t1 | TSS | g9272.t1 | 1385813 | 1385813 |
| chr_1 | g9272 | g9272.t1 | isoform | g9272.t1 | 1385908 | 1387224 |
| chr_1 | g9272 | g9272.t1 | exon | g9272.t1.exon1 | 1385908 | 1385940 |
| chr_1 | g9272 | g9272.t1 | cds | g9272.t1.CDS1 | 1385908 | 1385940 |
| chr_1 | g9272 | g9272.t1 | exon | g9272.t1.exon2 | 1386004 | 1386087 |
| chr_1 | g9272 | g9272.t1 | cds | g9272.t1.CDS2 | 1386004 | 1386087 |
| chr_1 | g9272 | g9272.t1 | exon | g9272.t1.exon3 | 1386241 | 1386337 |
| chr_1 | g9272 | g9272.t1 | cds | g9272.t1.CDS3 | 1386241 | 1386337 |
| chr_1 | g9272 | g9272.t1 | exon | g9272.t1.exon4 | 1386404 | 1386459 |
| chr_1 | g9272 | g9272.t1 | cds | g9272.t1.CDS4 | 1386404 | 1386459 |
| chr_1 | g9272 | g9272.t1 | exon | g9272.t1.exon5 | 1386515 | 1386707 |
| chr_1 | g9272 | g9272.t1 | cds | g9272.t1.CDS5 | 1386515 | 1386707 |
| chr_1 | g9272 | g9272.t1 | exon | g9272.t1.exon6 | 1386763 | 1386842 |
| chr_1 | g9272 | g9272.t1 | cds | g9272.t1.CDS6 | 1386763 | 1386842 |
| chr_1 | g9272 | g9272.t1 | exon | g9272.t1.exon7 | 1386904 | 1387224 |
| chr_1 | g9272 | g9272.t1 | cds | g9272.t1.CDS7 | 1386904 | 1387224 |
| chr_1 | g9272 | g9272.t1 | TTS | g9272.t1 | 1387250 | 1387250 |
Sequences
>g9272.t1 Gene=g9272 Length=864
ATGATTCGTGATCGACTTTATGAGTTAAGACCATTTAATACAGAAGAATCTATTGAAATT
GAAGTAGATACTTCAATGCAGAAACATGATGAAGAACTTTATAAAGTTTTAAATAGGTTT
CTTGTTATACGAGAACAAATTGATTTGATTCGACAAAATATTGATACCATGAAATCGTTA
ATTAATGAACAAAAGTTTCACTATAAGGATAAAAATATACGCGATCAAATAGAAAATTTA
ATAAGTGATAGTTTGTCAAAATCTAAAAATGTCCACAATTCAATCAAGTCATATCAAGAA
GAGTTAAAATTACCAAGTCAAAGTTATACAATATTTCGAATTAAAAATATGCAATTGGCA
CTCATTAAAAATGATTATTTAAATGTCTATAGAGAGCACACACTGTTTGTTGAAAAGTAT
GAGGAAAAATTGAAAAAAGTTTTAAAACGGGAAGCTCAAATTATGTCAAGAAATATTTCC
ATTGAGGAGACTGAAGCATTGATTGCAGAAAAAGAGCAAGTTCCCTCATTATTTGTGGGA
AATATTTTAGAAGAAACTGAAAAAGCACAATGTGAATTGCGAGAAATTGTTCAACGACAT
AATATGCTTATGACATTGGAAAAAACTTTAGAGGAAGTAAGAGATATGTTTTTTCAAATC
TCAACATATGTAATGGAGCAAGGTTCATTAATTCAAGTCATTGAATATGAAACTGAAAAT
GCAACAACTTATGTAGATAAAGGTGGCTCAGAATTAGAGAAAGCACGTGAATTGCAAATT
AAAGCTCTAAAGAAAAAGACCTATATCCTTATAATTCTTCTTATTGTATTAGGAATAATT
ATTTTGATTTTAATAATTACTTAA
>g9272.t1 Gene=g9272 Length=287
MIRDRLYELRPFNTEESIEIEVDTSMQKHDEELYKVLNRFLVIREQIDLIRQNIDTMKSL
INEQKFHYKDKNIRDQIENLISDSLSKSKNVHNSIKSYQEELKLPSQSYTIFRIKNMQLA
LIKNDYLNVYREHTLFVEKYEEKLKKVLKREAQIMSRNISIEETEALIAEKEQVPSLFVG
NILEETEKAQCELREIVQRHNMLMTLEKTLEEVRDMFFQISTYVMEQGSLIQVIEYETEN
ATTYVDKGGSELEKARELQIKALKKKTYILIILLIVLGIIILILIIT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9272.t1 | Coils | Coil | Coil | 137 | 157 | - |
| 6 | g9272.t1 | Gene3D | G3DSA:1.20.58.70 | - | 14 | 151 | 1.0E-6 |
| 7 | g9272.t1 | Gene3D | G3DSA:1.20.5.110 | - | 182 | 287 | 1.3E-24 |
| 3 | g9272.t1 | PANTHER | PTHR19957:SF19 | SYNTAXIN-4 | 30 | 286 | 1.4E-51 |
| 4 | g9272.t1 | PANTHER | PTHR19957 | SYNTAXIN | 30 | 286 | 1.4E-51 |
| 1 | g9272.t1 | Pfam | PF00804 | Syntaxin | 38 | 228 | 7.5E-20 |
| 2 | g9272.t1 | Pfam | PF05739 | SNARE domain | 230 | 281 | 1.1E-9 |
| 9 | g9272.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 267 | - |
| 11 | g9272.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 268 | 286 | - |
| 10 | g9272.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 287 | 287 | - |
| 14 | g9272.t1 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 198 | 255 | 13.494 |
| 13 | g9272.t1 | SMART | SM00397 | tSNARE_6 | 188 | 255 | 5.7E-9 |
| 5 | g9272.t1 | SUPERFAMILY | SSF47661 | t-snare proteins | 43 | 248 | 4.32E-29 |
| 12 | g9272.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 267 | 286 | - |
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: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.
