General information for g1200.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g1200.t1 | 8715762 | 8715762 |
| chr_3 | g1200 | g1200.t1 | isoform | g1200.t1 | 8715821 | 8716576 |
| chr_3 | g1200 | g1200.t1 | exon | g1200.t1.exon1 | 8715821 | 8715957 |
| chr_3 | g1200 | g1200.t1 | cds | g1200.t1.CDS1 | 8715821 | 8715957 |
| chr_3 | g1200 | g1200.t1 | exon | g1200.t1.exon2 | 8716018 | 8716576 |
| chr_3 | g1200 | g1200.t1 | cds | g1200.t1.CDS2 | 8716018 | 8716576 |
| chr_3 | g1200 | g1200.t1 | TTS | g1200.t1 | 8716734 | 8716734 |
Sequences
>g1200.t1 Gene=g1200 Length=696
ATGGCAGCAAAACTTGAAATAAATATAAGAAGTTTGTTAAGTACTTGTGAAGAGTTAGTA
AAAGAAGAAGATCAGAAATGGAAATTAACACGATATATAAAAAGCTTAGATTTAATGATC
AACGAATTGTCCGATTATGATACAGCAGATAAGAATCATATAGCAAAATACCAAGAAAAA
GTTCTAGAACTCAAAACACTTATTAATTATGTTGAACCACAAAAACAGAAAATAGTGAAA
ACTAGGAGGGATGTTGATGAGTCAGAAACAATTTTAAAGGAAATTAAGCAACTCAATAAC
GCAAAATTCAATAAAGAAATCAGAAAAGACTTATTTGATGGTGATGATGCAACAGGATTA
AGGAAAAGAGGGGCAAACGAAAGTTCAGAAAATATGGAAAGATATTATGATAATATTCAA
GAAAAATTAGGAGAAGAAATGCTTGCATTAACTAAAAATCTAAAAGAACAGTATTTAGCT
GCCAATAGCATAATTAAAAAAGATACAGAGGTCATAACTAAATCCGCAAAAATGGCTCAT
CAAAATATCGGATCACTAGAAAAAGAATCCAAAAAACTAAATGAGCATACAAAACGAGCA
TGTAAATGTTGGATGTGGATGATGATTGGTCTCGTAATTATGATATTTATCGCAATGGTC
CTATTCATGAAAATCATGAAGAAAAGGCAATATTAG
>g1200.t1 Gene=g1200 Length=231
MAAKLEINIRSLLSTCEELVKEEDQKWKLTRYIKSLDLMINELSDYDTADKNHIAKYQEK
VLELKTLINYVEPQKQKIVKTRRDVDESETILKEIKQLNNAKFNKEIRKDLFDGDDATGL
RKRGANESSENMERYYDNIQEKLGEEMLALTKNLKEQYLAANSIIKKDTEVITKSAKMAH
QNIGSLEKESKKLNEHTKRACKCWMWMMIGLVIMIFIAMVLFMKIMKKRQY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1200.t1 | CDD | cd15860 | SNARE_USE1 | 136 | 195 | 5.31412E-15 |
| 5 | g1200.t1 | Coils | Coil | Coil | 2 | 22 | - |
| 2 | g1200.t1 | PANTHER | PTHR13050 | USE1-LIKE PROTEIN | 1 | 229 | 2.3E-29 |
| 3 | g1200.t1 | PANTHER | PTHR13050:SF7 | VESICLE TRANSPORT PROTEIN USE1 | 1 | 229 | 2.3E-29 |
| 1 | g1200.t1 | Pfam | PF09753 | Membrane fusion protein Use1 | 4 | 226 | 9.6E-67 |
| 7 | g1200.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 203 | - |
| 8 | g1200.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 223 | - |
| 6 | g1200.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 224 | 231 | - |
| 4 | g1200.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 223 | - |
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 K08507 (unconventional SNARE in the endoplasmic reticulum protein 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.
