General information for g1200.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vesicle transport protein USE1.
Parent gene
- The parent gene g1200 is located on chr_3: 8715821..8716576 (+ 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 | g1200 | g1200.t11 | TSS | g1200.t11 | 8715762 | 8715762 |
| chr_3 | g1200 | g1200.t11 | isoform | g1200.t11 | 8715821 | 8716576 |
| chr_3 | g1200 | g1200.t11 | exon | g1200.t11.exon1 | 8715821 | 8715957 |
| chr_3 | g1200 | g1200.t11 | exon | g1200.t11.exon2 | 8716029 | 8716576 |
| chr_3 | g1200 | g1200.t11 | cds | g1200.t11.CDS1 | 8716274 | 8716576 |
| chr_3 | g1200 | g1200.t11 | TTS | g1200.t11 | 8716734 | 8716734 |
Sequences
>g1200.t11 Gene=g1200 Length=685
ATGGCAGCAAAACTTGAAATAAATATAAGAAGTTTGTTAAGTACTTGTGAAGAGTTAGTA
AAAGAAGAAGATCAGAAATGGAAATTAACACGATATATAAAAAGCTTAGATTTAATGATC
AACGAATTGTCCGATTAATAAGAATCATATAGCAAAATACCAAGAAAAAGTTCTAGAACT
CAAAACACTTATTAATTATGTTGAACCACAAAAACAGAAAATAGTGAAAACTAGGAGGGA
TGTTGATGAGTCAGAAACAATTTTAAAGGAAATTAAGCAACTCAATAACGCAAAATTCAA
TAAAGAAATCAGAAAAGACTTATTTGATGGTGATGATGCAACAGGATTAAGGAAAAGAGG
GGCAAACGAAAGTTCAGAAAATATGGAAAGATATTATGATAATATTCAAGAAAAATTAGG
AGAAGAAATGCTTGCATTAACTAAAAATCTAAAAGAACAGTATTTAGCTGCCAATAGCAT
AATTAAAAAAGATACAGAGGTCATAACTAAATCCGCAAAAATGGCTCATCAAAATATCGG
ATCACTAGAAAAAGAATCCAAAAAACTAAATGAGCATACAAAACGAGCATGTAAATGTTG
GATGTGGATGATGATTGGTCTCGTAATTATGATATTTATCGCAATGGTCCTATTCATGAA
AATCATGAAGAAAAGGCAATATTAG
>g1200.t11 Gene=g1200 Length=100
MERYYDNIQEKLGEEMLALTKNLKEQYLAANSIIKKDTEVITKSAKMAHQNIGSLEKESK
KLNEHTKRACKCWMWMMIGLVIMIFIAMVLFMKIMKKRQY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1200.t11 | CDD | cd15860 | SNARE_USE1 | 5 | 64 | 1.4068E-17 |
| 2 | g1200.t11 | PANTHER | PTHR13050 | USE1-LIKE PROTEIN | 7 | 98 | 8.1E-24 |
| 3 | g1200.t11 | PANTHER | PTHR13050:SF7 | VESICLE TRANSPORT PROTEIN USE1 | 7 | 98 | 8.1E-24 |
| 1 | g1200.t11 | Pfam | PF09753 | Membrane fusion protein Use1 | 3 | 95 | 4.9E-41 |
| 6 | g1200.t11 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 72 | - |
| 7 | g1200.t11 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 92 | - |
| 5 | g1200.t11 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 93 | 100 | - |
| 4 | g1200.t11 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 95 | - |
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 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.
