General information for g11024.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t9 | TTS | g11024.t9 | 13460240 | 13460240 |
| chr_1 | g11024 | g11024.t9 | isoform | g11024.t9 | 13460461 | 13461313 |
| chr_1 | g11024 | g11024.t9 | exon | g11024.t9.exon1 | 13460461 | 13460762 |
| chr_1 | g11024 | g11024.t9 | cds | g11024.t9.CDS1 | 13460759 | 13460762 |
| chr_1 | g11024 | g11024.t9 | exon | g11024.t9.exon2 | 13460816 | 13460938 |
| chr_1 | g11024 | g11024.t9 | cds | g11024.t9.CDS2 | 13460816 | 13460938 |
| chr_1 | g11024 | g11024.t9 | exon | g11024.t9.exon3 | 13461028 | 13461179 |
| chr_1 | g11024 | g11024.t9 | cds | g11024.t9.CDS3 | 13461028 | 13461179 |
| chr_1 | g11024 | g11024.t9 | exon | g11024.t9.exon4 | 13461245 | 13461313 |
| chr_1 | g11024 | g11024.t9 | cds | g11024.t9.CDS4 | 13461245 | 13461313 |
| chr_1 | g11024 | g11024.t9 | TSS | g11024.t9 | 13461386 | 13461386 |
Sequences
>g11024.t9 Gene=g11024 Length=646
ATGAATCGCTTATTTGGAAGAGGTAAACCAAAAGAACCACCACCAGACCTCAATGAATGC
ATTGGAAAAGTGGATTCTCGAGCTGAAGGAATTGAAAAGAAAATTCAAATTCTAGACAAT
GAATTGCGTAAATACAAAGATCAAATGGCTAAAATGAGAGAAGGACCGAGCAAGAATGCA
GTGAAACAGAAAGCTCTTCGTGTTTTAAAGCAAAAGAAACAATATGAGCAGCAAGTTGAA
AGTTTAAGAAATCAGTCATTCAATATGGAACAAGCTAATTATGCGAATCAGATGATGAAA
GATACTCAAGCAACTGTTGTCGCAATGAAAGATGGAATGAAATCATGACATGGCTGATAT
GCTTGAACAAGCAGATGAAGTCCAAGAAGCTCTTGGAAGAAATTACAACATGCCTGAAAT
TGATGAAGATGATCTGCAAGCAGAACTCGATGCATTGGGTGATGAAATTGCATTGGACGA
TGATAGTAGTTATTTGGATGATGTTATTAAAGCACCAGGTATTCCAGACAAAGAACCTGG
AGCTGATAGCGTCGTTGCACCGCCTTCAAAAACAAAGGATGGAATTTTAGTCGATGAATT
TGGTTTACCACAACTACCTGCAGCTTCATCATCTAAACAAAACTAA
>g11024.t9 Gene=g11024 Length=115
MNRLFGRGKPKEPPPDLNECIGKVDSRAEGIEKKIQILDNELRKYKDQMAKMREGPSKNA
VKQKALRVLKQKKQYEQQVESLRNQSFNMEQANYANQMMKDTQATVVAMKDGMKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11024.t9 | Coils | Coil | Coil | 28 | 55 | - |
| 7 | g11024.t9 | Coils | Coil | Coil | 58 | 92 | - |
| 5 | g11024.t9 | Gene3D | G3DSA:1.10.287.1060 | - | 17 | 95 | 9.1E-6 |
| 4 | g11024.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 2 | g11024.t9 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 1 | 114 | 1.2E-47 |
| 3 | g11024.t9 | PANTHER | PTHR22761:SF69 | CHARGED MULTIVESICULAR BODY PROTEIN 5 | 1 | 114 | 1.2E-47 |
| 1 | g11024.t9 | Pfam | PF03357 | Snf7 | 12 | 114 | 1.0E-23 |
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.
