General information for g10379.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g10379 is located on chr_1: 9330286..9348435 (- 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 | g10379 | g10379.t2 | isoform | g10379.t2 | 9329717 | 9330286 |
| chr_1 | g10379 | g10379.t2 | exon | g10379.t2.exon1 | 9329717 | 9330119 |
| chr_1 | g10379 | g10379.t2 | cds | g10379.t2.CDS1 | 9329877 | 9330119 |
| chr_1 | g10379 | g10379.t2 | exon | g10379.t2.exon2 | 9330188 | 9330286 |
| chr_1 | g10379 | g10379.t2 | cds | g10379.t2.CDS2 | 9330188 | 9330286 |
| chr_1 | g10379 | g10379.t2 | TSS | g10379.t2 | 9330354 | 9330354 |
| chr_1 | g10379 | g10379.t2 | TTS | g10379.t2 | NA | NA |
Sequences
>g10379.t2 Gene=g10379 Length=502
ATGTCCAACTATGATTGGGATTCACATAATAGACAGGCTATGCTTGAAGGAAGACAGATA
CTTGAAAGAACAACAGCATCATTGGCTAGAAGCAATCAAATTGCTATTGATACAGAAAAT
ACAGGTACAGAAATATTGACAGAGTTAGACAGTCAAAGAGAAGCTCTTTTACGAACAAGT
GAAAGATTGGACAACGCAAATGATGGATTATCTGCAAGTAATAAAATTATGCGAACAATG
GTGCGAACAGCACTTTATAATAAACTCATATTAATTTTAATAATAGTATTAGAAGTTTTT
ATATTAGCTTGTATGATCTATATGAAATTCATTCACAAATAAAATTTTAAAGATATGAGA
GTTCATTTTATTTCATCATATGTTATTATTTGAAGGTGGCTTTGCCTACGACTTGCCTTC
GATGAAGAAAAATCTTCAAAGACCGAAGATACCTTCAAATAACAACTGGTTCATCACTGA
CATGGAAAAGTCGAAAAAATAA
>g10379.t2 Gene=g10379 Length=113
MSNYDWDSHNRQAMLEGRQILERTTASLARSNQIAIDTENTGTEILTELDSQREALLRTS
ERLDNANDGLSASNKIMRTMVRTALYNKLILILIIVLEVFILACMIYMKFIHK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g10379.t2 | CDD | cd15890 | SNARE_Vti1b | 18 | 78 | 5.74097E-18 |
| 6 | g10379.t2 | Coils | Coil | Coil | 46 | 66 | - |
| 5 | g10379.t2 | Gene3D | G3DSA:1.20.5.110 | - | 9 | 88 | 3.7E-22 |
| 2 | g10379.t2 | PANTHER | PTHR21230:SF79 | VESICLE TRANSPORT THROUGH INTERACTION WITH T-SNARES HOMOLOG 1B | 9 | 110 | 3.7E-21 |
| 3 | g10379.t2 | PANTHER | PTHR21230 | VESICLE TRANSPORT V-SNARE PROTEIN VTI1-RELATED | 9 | 110 | 3.7E-21 |
| 1 | g10379.t2 | Pfam | PF12352 | Snare region anchored in the vesicle membrane C-terminus | 20 | 82 | 4.0E-15 |
| 7 | g10379.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 84 | - |
| 9 | g10379.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 85 | 108 | - |
| 8 | g10379.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 109 | 113 | - |
| 12 | g10379.t2 | SMART | SM00397 | tSNARE_6 | 13 | 80 | 0.002 |
| 4 | g10379.t2 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 8 | 80 | 9.3E-16 |
| 11 | g10379.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 89 | 111 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K08493 (vesicle transport through interaction with t-SNAREs 1)
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.
