General information for g11024.t1
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.t1 | TTS | g11024.t1 | 13460240 | 13460240 |
| chr_1 | g11024 | g11024.t1 | isoform | g11024.t1 | 13460461 | 13461313 |
| chr_1 | g11024 | g11024.t1 | exon | g11024.t1.exon1 | 13460461 | 13460938 |
| chr_1 | g11024 | g11024.t1 | cds | g11024.t1.CDS1 | 13460461 | 13460938 |
| chr_1 | g11024 | g11024.t1 | exon | g11024.t1.exon2 | 13461028 | 13461179 |
| chr_1 | g11024 | g11024.t1 | cds | g11024.t1.CDS2 | 13461028 | 13461179 |
| chr_1 | g11024 | g11024.t1 | exon | g11024.t1.exon3 | 13461245 | 13461313 |
| chr_1 | g11024 | g11024.t1 | cds | g11024.t1.CDS3 | 13461245 | 13461313 |
| chr_1 | g11024 | g11024.t1 | TSS | g11024.t1 | 13461386 | 13461386 |
Sequences
>g11024.t1 Gene=g11024 Length=699
ATGAATCGCTTATTTGGAAGAGGTAAACCAAAAGAACCACCACCAGACCTCAATGAATGC
ATTGGAAAAGTGGATTCTCGAGCTGAAGGAATTGAAAAGAAAATTCAAATTCTAGACAAT
GAATTGCGTAAATACAAAGATCAAATGGCTAAAATGAGAGAAGGACCGAGCAAGAATGCA
GTGAAACAGAAAGCTCTTCGTGTTTTAAAGCAAAAGAAACAATATGAGCAGCAAGTTGAA
AGTTTAAGAAATCAGTCATTCAATATGGAACAAGCTAATTATGCGAATCAGATGATGAAA
GATACTCAAGCAACTGTTGTCGCAATGAAAGATGGAATGAAATCTATGAAAAAAGAATTT
AAGAAGATTAACATTGAAGATATTGAAGATCTTCAAGATGACATGGCTGATATGCTTGAA
CAAGCAGATGAAGTCCAAGAAGCTCTTGGAAGAAATTACAACATGCCTGAAATTGATGAA
GATGATCTGCAAGCAGAACTCGATGCATTGGGTGATGAAATTGCATTGGACGATGATAGT
AGTTATTTGGATGATGTTATTAAAGCACCAGGTATTCCAGACAAAGAACCTGGAGCTGAT
AGCGTCGTTGCACCGCCTTCAAAAACAAAGGATGGAATTTTAGTCGATGAATTTGGTTTA
CCACAACTACCTGCAGCTTCATCATCTAAACAAAACTAA
>g11024.t1 Gene=g11024 Length=232
MNRLFGRGKPKEPPPDLNECIGKVDSRAEGIEKKIQILDNELRKYKDQMAKMREGPSKNA
VKQKALRVLKQKKQYEQQVESLRNQSFNMEQANYANQMMKDTQATVVAMKDGMKSMKKEF
KKINIEDIEDLQDDMADMLEQADEVQEALGRNYNMPEIDEDDLQAELDALGDEIALDDDS
SYLDDVIKAPGIPDKEPGADSVVAPPSKTKDGILVDEFGLPQLPAASSSKQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11024.t1 | Coils | Coil | Coil | 28 | 55 | - |
| 9 | g11024.t1 | Coils | Coil | Coil | 58 | 92 | - |
| 7 | g11024.t1 | Coils | Coil | Coil | 128 | 148 | - |
| 6 | g11024.t1 | Gene3D | G3DSA:1.10.287.1060 | - | 17 | 95 | 5.0E-5 |
| 5 | g11024.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 4 | g11024.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 210 | - |
| 2 | g11024.t1 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 1 | 223 | 6.2E-83 |
| 3 | g11024.t1 | PANTHER | PTHR22761:SF69 | CHARGED MULTIVESICULAR BODY PROTEIN 5 | 1 | 223 | 6.2E-83 |
| 1 | g11024.t1 | Pfam | PF03357 | Snf7 | 12 | 196 | 2.2E-49 |
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.
