General information for g9223.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g9223.t1 | 904496 | 904496 |
| chr_1 | g9223 | g9223.t1 | isoform | g9223.t1 | 904571 | 905233 |
| chr_1 | g9223 | g9223.t1 | exon | g9223.t1.exon1 | 904571 | 904832 |
| chr_1 | g9223 | g9223.t1 | cds | g9223.t1.CDS1 | 904571 | 904832 |
| chr_1 | g9223 | g9223.t1 | exon | g9223.t1.exon2 | 904896 | 905233 |
| chr_1 | g9223 | g9223.t1 | cds | g9223.t1.CDS2 | 904896 | 905233 |
| chr_1 | g9223 | g9223.t1 | TTS | g9223.t1 | 905552 | 905552 |
Sequences
>g9223.t1 Gene=g9223 Length=600
ATGGTAAAAATATACGCTATCAGTATCTTCTACAAATCAGCAAATGAAGCCAAAATATTG
AAATCTCACTATGATCTGCAGAGCTTTAGTTTTTTTCAAAGAGGCAGCGTTCAAGAATTT
ATTCAATTTGCAAGCAAAACAATTGTTGAGCGAACAAGTCCATGTACTCGTCAATCAGTT
AAACAAGATGTTTATATGTGTCACGTTTATGTGAGATCTGATAATTTGGCAGCAGTTCTT
ATTGCAGATCATGAATATCCAGGGCGTGTGGCACATACTCTTTTAACAAAGATCATGGAT
GATTTTGCAGCAAAAGTTTCAAGCCCAGAATGGCCAAATGGTACAGAACAAACGATTAAT
TTTACTCAGCTTCCAGCTTATATCGCCAAATATCAAGATCCCCGTGAAGCTGACCCTTTG
ACAAAAATGCAAAATGACTTGGATGAGACGAAGATTATTTTGAAAAATACTATCGAGCAA
GTTTTAATAAGAGGAGAAAAATTAGACGATTTAGTTAGTCAATCTGAAGAGCTATCAGCG
CAGTCAAAAGCTTTTTATAAAACTGCTAAAAAGACAAATTCCTGTTGTAATTTTAGTTAA
>g9223.t1 Gene=g9223 Length=199
MVKIYAISIFYKSANEAKILKSHYDLQSFSFFQRGSVQEFIQFASKTIVERTSPCTRQSV
KQDVYMCHVYVRSDNLAAVLIADHEYPGRVAHTLLTKIMDDFAAKVSSPEWPNGTEQTIN
FTQLPAYIAKYQDPREADPLTKMQNDLDETKIILKNTIEQVLIRGEKLDDLVSQSEELSA
QSKAFYKTAKKTNSCCNFS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g9223.t1 | CDD | cd14824 | Longin | 5 | 131 | 1.00138E-29 |
| 9 | g9223.t1 | Coils | Coil | Coil | 140 | 160 | - |
| 8 | g9223.t1 | Gene3D | G3DSA:3.30.450.50 | - | 1 | 138 | 1.5E-55 |
| 7 | g9223.t1 | Gene3D | G3DSA:1.20.5.110 | - | 142 | 198 | 9.4E-29 |
| 3 | g9223.t1 | PANTHER | PTHR45806:SF1 | SYNAPTOBREVIN HOMOLOG YKT6 | 1 | 198 | 7.7E-77 |
| 4 | g9223.t1 | PANTHER | PTHR45806 | SYNAPTOBREVIN HOMOLOG YKT6 | 1 | 198 | 7.7E-77 |
| 1 | g9223.t1 | Pfam | PF13774 | Regulated-SNARE-like domain | 46 | 127 | 3.6E-11 |
| 2 | g9223.t1 | Pfam | PF00957 | Synaptobrevin | 137 | 193 | 1.9E-13 |
| 13 | g9223.t1 | ProSiteProfiles | PS50859 | Longin domain profile. | 9 | 128 | 22.503 |
| 12 | g9223.t1 | ProSiteProfiles | PS50892 | v-SNARE coiled-coil homology domain profile. | 139 | 199 | 14.577 |
| 11 | g9223.t1 | SMART | SM01270 | Longin_2 | 44 | 135 | 1.8E-23 |
| 5 | g9223.t1 | SUPERFAMILY | SSF64356 | SNARE-like | 2 | 138 | 2.33E-44 |
| 6 | g9223.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 133 | 197 | 2.41E-17 |
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 transcript has been annotated with K08516 (synaptobrevin homolog YKT6)
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.
