General information for g11024.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Charged multivesicular body protein 5.
Parent gene
- The parent gene g11024 is located on chr_1: 13460461..13461313 (- 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 | g11024 | g11024.t13 | TTS | g11024.t13 | 13460240 | 13460240 |
| chr_1 | g11024 | g11024.t13 | isoform | g11024.t13 | 13460461 | 13461313 |
| chr_1 | g11024 | g11024.t13 | exon | g11024.t13.exon1 | 13460461 | 13460938 |
| chr_1 | g11024 | g11024.t13 | cds | g11024.t13.CDS1 | 13460461 | 13460938 |
| chr_1 | g11024 | g11024.t13 | exon | g11024.t13.exon2 | 13461028 | 13461166 |
| chr_1 | g11024 | g11024.t13 | cds | g11024.t13.CDS2 | 13461028 | 13461166 |
| chr_1 | g11024 | g11024.t13 | exon | g11024.t13.exon3 | 13461235 | 13461313 |
| chr_1 | g11024 | g11024.t13 | cds | g11024.t13.CDS3 | 13461235 | 13461313 |
| chr_1 | g11024 | g11024.t13 | TSS | g11024.t13 | 13461386 | 13461386 |
Sequences
>g11024.t13 Gene=g11024 Length=696
ATGAATCGCTTATTTGGAAGAGGTAAACCAAAAGAACCACCACCAGACCTCAATGAATGC
ATTGGAAAAGTAAGTGAATCTGAAGGAATTGAAAAGAAAATTCAAATTCTAGACAATGAA
TTGCGTAAATACAAAGATCAAATGGCTAAAATGAGAGAAGGACCGAGCAAGAATGCAGTG
AAACAGAAAGCTCTTCGTGTTTTAAAGCAAAAGAAACAATATGAGCAGCAAGTTGAAAGT
TTAAGAAATCAGTCATTCAATATGGAACAAGCTAATTATGCGAATCAGATGATGAAAGAT
ACTCAAGCAACTGTTGTCGCAATGAAAGATGGAATGAAATCTATGAAAAAAGAATTTAAG
AAGATTAACATTGAAGATATTGAAGATCTTCAAGATGACATGGCTGATATGCTTGAACAA
GCAGATGAAGTCCAAGAAGCTCTTGGAAGAAATTACAACATGCCTGAAATTGATGAAGAT
GATCTGCAAGCAGAACTCGATGCATTGGGTGATGAAATTGCATTGGACGATGATAGTAGT
TATTTGGATGATGTTATTAAAGCACCAGGTATTCCAGACAAAGAACCTGGAGCTGATAGC
GTCGTTGCACCGCCTTCAAAAACAAAGGATGGAATTTTAGTCGATGAATTTGGTTTACCA
CAACTACCTGCAGCTTCATCATCTAAACAAAACTAA
>g11024.t13 Gene=g11024 Length=231
MNRLFGRGKPKEPPPDLNECIGKVSESEGIEKKIQILDNELRKYKDQMAKMREGPSKNAV
KQKALRVLKQKKQYEQQVESLRNQSFNMEQANYANQMMKDTQATVVAMKDGMKSMKKEFK
KINIEDIEDLQDDMADMLEQADEVQEALGRNYNMPEIDEDDLQAELDALGDEIALDDDSS
YLDDVIKAPGIPDKEPGADSVVAPPSKTKDGILVDEFGLPQLPAASSSKQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11024.t13 | Coils | Coil | Coil | 27 | 54 | - |
| 7 | g11024.t13 | Coils | Coil | Coil | 57 | 91 | - |
| 8 | g11024.t13 | Coils | Coil | Coil | 127 | 147 | - |
| 5 | g11024.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 16 | - |
| 6 | g11024.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 4 | g11024.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 209 | - |
| 2 | g11024.t13 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 1 | 222 | 9.7E-79 |
| 3 | g11024.t13 | PANTHER | PTHR22761:SF69 | CHARGED MULTIVESICULAR BODY PROTEIN 5 | 1 | 222 | 9.7E-79 |
| 1 | g11024.t13 | Pfam | PF03357 | Snf7 | 12 | 195 | 1.1E-46 |
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 K12198 (charged multivesicular body protein 5)
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. There were no conditions that were differentially expressed