General information for g1857.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Charged multivesicular body protein 3.
Parent gene
- The parent gene g1857 is located on chr_3: 13404554..13405913 (+ 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 | g1857 | g1857.t1 | TSS | g1857.t1 | 13404257 | 13404257 |
| chr_3 | g1857 | g1857.t1 | isoform | g1857.t1 | 13404554 | 13405385 |
| chr_3 | g1857 | g1857.t1 | exon | g1857.t1.exon1 | 13404554 | 13404598 |
| chr_3 | g1857 | g1857.t1 | cds | g1857.t1.CDS1 | 13404554 | 13404598 |
| chr_3 | g1857 | g1857.t1 | exon | g1857.t1.exon2 | 13404695 | 13404935 |
| chr_3 | g1857 | g1857.t1 | cds | g1857.t1.CDS2 | 13404695 | 13404935 |
| chr_3 | g1857 | g1857.t1 | exon | g1857.t1.exon3 | 13405012 | 13405385 |
| chr_3 | g1857 | g1857.t1 | cds | g1857.t1.CDS3 | 13405012 | 13405385 |
| chr_3 | g1857 | g1857.t1 | TTS | g1857.t1 | 13405790 | 13405790 |
Sequences
>g1857.t1 Gene=g1857 Length=660
ATGGGTTTATTTGGTCAATCAAAACAAAAGAATCCACAAGAAATGGTAAAAGAGTGGAAC
GCAAAATTGCGCAAAGAGGGTTACGCACTTGATCGTCAAATACGCTCAATAAAACGAGAA
GAAGATAAAATAAAGAAATCACTTAAAGAGGCTGCAAAGAAAAATGATAAACAAGTTTGC
TCTATTTTAGCAAAGGAAGTTGTCAGATCCAGAAGAGCTGTGAATCGAATTTATGCTAGT
AAAGCTACTCTAAGTTCTGTGCAATTGCAAATGGCACAACAAATGGCAACACTTAAAGTC
TCTGGATCACTTCAAAAATCTACAGAAGTAATGGCTGCAATGCAAAAACTCGTCAAACTA
CCCGAAATTTCCAATACAATGCGTGAAATGTCAAGGGAAATGACCAAAGCCGGAATTCTT
GAGGAGATGATTGAAGAAACAATGGAATCTCTAGAAGATTCAGAAGAAATTGAAGAGGAA
GCACAAGGTGAAGTAGATAAAGTATTATGGGAGCTTACAGATGGCAAACTTGGTGAAGCA
CCTGCTGTTCCAATAAGCACGCCTAATGAACCTGCAGCAAGTACTGCTGTTCAAGATGAT
GAAGATGAAGAAGAAGAACTTGAGGATATGAAGAGTCGATTGGAAGCATTGCGATCTTAA
>g1857.t1 Gene=g1857 Length=219
MGLFGQSKQKNPQEMVKEWNAKLRKEGYALDRQIRSIKREEDKIKKSLKEAAKKNDKQVC
SILAKEVVRSRRAVNRIYASKATLSSVQLQMAQQMATLKVSGSLQKSTEVMAAMQKLVKL
PEISNTMREMSREMTKAGILEEMIEETMESLEDSEEIEEEAQGEVDKVLWELTDGKLGEA
PAVPISTPNEPAASTAVQDDEDEEEELEDMKSRLEALRS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1857.t1 | Coils | Coil | Coil | 30 | 57 | - |
| 7 | g1857.t1 | Coils | Coil | Coil | 140 | 164 | - |
| 5 | g1857.t1 | Coils | Coil | Coil | 197 | 219 | - |
| 4 | g1857.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 178 | 219 | - |
| 2 | g1857.t1 | PANTHER | PTHR10476:SF1 | CHARGED MULTIVESICULAR BODY PROTEIN 3 | 8 | 219 | 1.1E-79 |
| 3 | g1857.t1 | PANTHER | PTHR10476 | CHARGED MULTIVESICULAR BODY PROTEIN | 8 | 219 | 1.1E-79 |
| 1 | g1857.t1 | Pfam | PF03357 | Snf7 | 18 | 184 | 3.4E-37 |
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:0007034 | vacuolar transport | BP |
KEGG
Orthology
- This transcript has been annotated with K12193 (charged multivesicular body protein 3)
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.
