General information for g11024.t3
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.t3 | TTS | g11024.t3 | 13460240 | 13460240 |
| chr_1 | g11024 | g11024.t3 | isoform | g11024.t3 | 13460461 | 13461313 |
| chr_1 | g11024 | g11024.t3 | exon | g11024.t3.exon1 | 13460461 | 13460938 |
| chr_1 | g11024 | g11024.t3 | cds | g11024.t3.CDS1 | 13460461 | 13460938 |
| chr_1 | g11024 | g11024.t3 | exon | g11024.t3.exon2 | 13461028 | 13461313 |
| chr_1 | g11024 | g11024.t3 | cds | g11024.t3.CDS2 | 13461028 | 13461236 |
| chr_1 | g11024 | g11024.t3 | TSS | g11024.t3 | 13461386 | 13461386 |
Sequences
>g11024.t3 Gene=g11024 Length=764
ATGAATCGCTTATTTGGAAGAGGTAAACCAAAAGAACCACCACCAGACCTCAATGAATGC
ATTGGAAAAGTAAGTGAATGTATATGAACACAAAATATTTTTATCATAAACTAAAATCAA
TTGATTTTTCTAAGGTGGATTCTCGAGCTGAAGGAATTGAAAAGAAAATTCAAATTCTAG
ACAATGAATTGCGTAAATACAAAGATCAAATGGCTAAAATGAGAGAAGGACCGAGCAAGA
ATGCAGTGAAACAGAAAGCTCTTCGTGTTTTAAAGCAAAAGAAACAATATGAGCAGCAAG
TTGAAAGTTTAAGAAATCAGTCATTCAATATGGAACAAGCTAATTATGCGAATCAGATGA
TGAAAGATACTCAAGCAACTGTTGTCGCAATGAAAGATGGAATGAAATCTATGAAAAAAG
AATTTAAGAAGATTAACATTGAAGATATTGAAGATCTTCAAGATGACATGGCTGATATGC
TTGAACAAGCAGATGAAGTCCAAGAAGCTCTTGGAAGAAATTACAACATGCCTGAAATTG
ATGAAGATGATCTGCAAGCAGAACTCGATGCATTGGGTGATGAAATTGCATTGGACGATG
ATAGTAGTTATTTGGATGATGTTATTAAAGCACCAGGTATTCCAGACAAAGAACCTGGAG
CTGATAGCGTCGTTGCACCGCCTTCAAAAACAAAGGATGGAATTTTAGTCGATGAATTTG
GTTTACCACAACTACCTGCAGCTTCATCATCTAAACAAAACTAA
>g11024.t3 Gene=g11024 Length=228
MYMNTKYFYHKLKSIDFSKVDSRAEGIEKKIQILDNELRKYKDQMAKMREGPSKNAVKQK
ALRVLKQKKQYEQQVESLRNQSFNMEQANYANQMMKDTQATVVAMKDGMKSMKKEFKKIN
IEDIEDLQDDMADMLEQADEVQEALGRNYNMPEIDEDDLQAELDALGDEIALDDDSSYLD
DVIKAPGIPDKEPGADSVVAPPSKTKDGILVDEFGLPQLPAASSSKQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11024.t3 | Coils | Coil | Coil | 24 | 51 | - |
| 5 | g11024.t3 | Coils | Coil | Coil | 54 | 88 | - |
| 7 | g11024.t3 | Coils | Coil | Coil | 124 | 144 | - |
| 4 | g11024.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 186 | 206 | - |
| 2 | g11024.t3 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 17 | 219 | 3.1E-72 |
| 3 | g11024.t3 | PANTHER | PTHR22761:SF69 | CHARGED MULTIVESICULAR BODY PROTEIN 5 | 17 | 219 | 3.1E-72 |
| 1 | g11024.t3 | Pfam | PF03357 | Snf7 | 19 | 192 | 9.1E-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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
