General information for g9223.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Synaptobrevin homolog YKT6.
Parent gene
- The parent gene g9223 is located on chr_1: 904912..905594 (+ 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 | g9223 | g9223.t10 | TSS | g9223.t10 | 904496 | 904496 |
| chr_1 | g9223 | g9223.t10 | isoform | g9223.t10 | 904912 | 905594 |
| chr_1 | g9223 | g9223.t10 | exon | g9223.t10.exon1 | 904912 | 905594 |
| chr_1 | g9223 | g9223.t10 | cds | g9223.t10.CDS1 | 904928 | 905233 |
| chr_1 | g9223 | g9223.t10 | TTS | g9223.t10 | 905552 | 905552 |
Sequences
>g9223.t10 Gene=g9223 Length=683
TCTTTTAACAAAGATCATGGATGATTTTGCAGCAAAAGTTTCAAGCCCAGAATGGCCAAA
TGGTACAGAACAAACGATTAATTTTACTCAGCTTCCAGCTTATATCGCCAAATATCAAGA
TCCCCGTGAAGCTGACCCTTTGACAAAAATGCAAAATGACTTGGATGAGACGAAGATTAT
TTTGAAAAATACTATCGAGCAAGTTTTAATAAGAGGAGAAAAATTAGACGATTTAGTTAG
TCAATCTGAAGAGCTATCAGCGCAGTCAAAAGCTTTTTATAAAACTGCTAAAAAGACAAA
TTCCTGTTGTAATTTTAGTTAAATTGTCACACTCATTTAAAAGAAACATTACCATGATTT
TAATATATTCCTAATGTTTTATTTTTATAATCATATAAAGAACATGAGAAGAAGAGTTTT
AAGTCATTATATTAATTTATCCCACATACTATCAATTCTCAATGTTTTTCGTCGCATGCA
TATTACTGTCATAGACATTTTAATTAAATGGATAATTGTGAGCAAGCAGACACTAAAAAT
ATATCCTTTTCAAGATATTACATACATATTTAGATAAAATGCGCAGATTAAATTATAAAT
AATAAAAATTTATTAATAATCATAAATGTAAAATAAAGTATGTATTTTCTTATATCATGA
TTGAACAAAATCACTTGATTTTT
>g9223.t10 Gene=g9223 Length=101
MDDFAAKVSSPEWPNGTEQTINFTQLPAYIAKYQDPREADPLTKMQNDLDETKIILKNTI
EQVLIRGEKLDDLVSQSEELSAQSKAFYKTAKKTNSCCNFS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9223.t10 | Coils | Coil | Coil | 42 | 62 | - |
| 7 | g9223.t10 | Gene3D | G3DSA:3.30.450.50 | - | 1 | 43 | 9.3E-8 |
| 6 | g9223.t10 | Gene3D | G3DSA:1.20.5.110 | - | 44 | 100 | 2.0E-29 |
| 2 | g9223.t10 | PANTHER | PTHR45806:SF1 | SYNAPTOBREVIN HOMOLOG YKT6 | 1 | 100 | 1.2E-36 |
| 3 | g9223.t10 | PANTHER | PTHR45806 | SYNAPTOBREVIN HOMOLOG YKT6 | 1 | 100 | 1.2E-36 |
| 1 | g9223.t10 | Pfam | PF00957 | Synaptobrevin | 39 | 95 | 4.0E-14 |
| 9 | g9223.t10 | ProSiteProfiles | PS50892 | v-SNARE coiled-coil homology domain profile. | 41 | 101 | 14.577 |
| 4 | g9223.t10 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 40 | 3.75E-5 |
| 5 | g9223.t10 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 35 | 99 | 4.4E-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: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.
