General information for g13645.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Charged multivesicular body protein 6.
Parent gene
- The parent gene g13645 is located on chr_1: 31402887..31403743 (- 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 | g13645 | g13645.t1 | TTS | g13645.t1 | 31402594 | 31402594 |
| chr_1 | g13645 | g13645.t1 | isoform | g13645.t1 | 31402887 | 31403656 |
| chr_1 | g13645 | g13645.t1 | exon | g13645.t1.exon1 | 31402887 | 31403346 |
| chr_1 | g13645 | g13645.t1 | cds | g13645.t1.CDS1 | 31402887 | 31403346 |
| chr_1 | g13645 | g13645.t1 | exon | g13645.t1.exon2 | 31403415 | 31403524 |
| chr_1 | g13645 | g13645.t1 | cds | g13645.t1.CDS2 | 31403415 | 31403524 |
| chr_1 | g13645 | g13645.t1 | exon | g13645.t1.exon3 | 31403588 | 31403656 |
| chr_1 | g13645 | g13645.t1 | cds | g13645.t1.CDS3 | 31403588 | 31403656 |
| chr_1 | g13645 | g13645.t1 | TSS | g13645.t1 | 31403765 | 31403765 |
Sequences
>g13645.t1 Gene=g13645 Length=639
ATGGGTGGAATATTTGGAAAATCTAAAAAACAACCGAGTCGAGTTACTGAACAGGATAAA
GCGGTTTTACAATTGAAGCAACAGAGAGATAAAATAAAGCAGTATCAAAAAAGAATTGAA
CAATCATTAGAAAAAGATCGTGCATTAGCAATTCAATGTTTGAACAAAGGACAAAGAGAG
CGTGCAAAATTAATTTTGCGTAAGAAAAAATATCAAGAGAATTTATTGGCCACTACTGAC
AAAGAACTTGAAACACTTGAAAAGTTAACATCTGATTTGGAATTCTCTCAAGTTCAGCAA
CAAGTAATTGATGGTCTTAAGGTTGGTAACGAAGCGCTCAAGAAAATTCACGAAGTGCTC
ACTATTGAGGAAGTTGAAAGAATTATGGATGAATCAAGAGAAGGAGTTGAGAAGCAGCAA
GAAATTGATACATTGATTGCATCAGGAATACTTAGTTCAGAAGATGAAGATGCTGTTGCA
GCTGAGTTGGAAGAATTGGTTGCCAGTACATTGCCTGCTATTGATGAAGATATCGATGAA
AAGTTGCCCGAAATACCAACAGAAGAACCAGAAATCGAGAAGAAAAAAAAGAAGGAGAAA
GAACGTCATCAAGAAGAGCGTGTAGCGCTTGAAGCTTAA
>g13645.t1 Gene=g13645 Length=212
MGGIFGKSKKQPSRVTEQDKAVLQLKQQRDKIKQYQKRIEQSLEKDRALAIQCLNKGQRE
RAKLILRKKKYQENLLATTDKELETLEKLTSDLEFSQVQQQVIDGLKVGNEALKKIHEVL
TIEEVERIMDESREGVEKQQEIDTLIASGILSSEDEDAVAAELEELVASTLPAIDEDIDE
KLPEIPTEEPEIEKKKKKEKERHQEERVALEA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13645.t1 | Coils | Coil | Coil | 18 | 45 | - |
| 9 | g13645.t1 | Coils | Coil | Coil | 54 | 74 | - |
| 8 | g13645.t1 | Coils | Coil | Coil | 122 | 142 | - |
| 6 | g13645.t1 | Coils | Coil | Coil | 193 | 212 | - |
| 4 | g13645.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 5 | g13645.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 177 | 212 | - |
| 2 | g13645.t1 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 3 | 201 | 2.6E-49 |
| 3 | g13645.t1 | PANTHER | PTHR22761:SF5 | CHARGED MULTIVESICULAR BODY PROTEIN 6 | 3 | 201 | 2.6E-49 |
| 1 | g13645.t1 | Pfam | PF03357 | Snf7 | 21 | 189 | 1.1E-35 |
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 K12195 (charged multivesicular body protein 6)
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.
