General information for g6276.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 g6276 is located on chr_2: 15776258..15777098 (- 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_2 | g6276 | g6276.t1 | TTS | g6276.t1 | 15776196 | 15776196 |
| chr_2 | g6276 | g6276.t1 | isoform | g6276.t1 | 15776258 | 15777098 |
| chr_2 | g6276 | g6276.t1 | exon | g6276.t1.exon1 | 15776258 | 15776735 |
| chr_2 | g6276 | g6276.t1 | cds | g6276.t1.CDS1 | 15776258 | 15776735 |
| chr_2 | g6276 | g6276.t1 | exon | g6276.t1.exon2 | 15776820 | 15776971 |
| chr_2 | g6276 | g6276.t1 | cds | g6276.t1.CDS2 | 15776820 | 15776971 |
| chr_2 | g6276 | g6276.t1 | exon | g6276.t1.exon3 | 15777030 | 15777098 |
| chr_2 | g6276 | g6276.t1 | cds | g6276.t1.CDS3 | 15777030 | 15777098 |
| chr_2 | g6276 | g6276.t1 | TSS | g6276.t1 | 15777197 | 15777197 |
Sequences
>g6276.t1 Gene=g6276 Length=699
ATGCATCGCTTATTTGGAAGAGGTAAACCAAAAAAACCACCACCAAATCTCAATGAATGC
ATTGGAAAAGTGGATTCTCGTGTTGAAGGAATTGAGAAGAAAATTCAAATTCTAGATAAT
AAATTGCGTAAATACAAGGATCAAATGGCTAAAATAAAAGAAGGACCGAGCATGAATGCA
TTGAAACAGAAAGCTCTTTGCGTTTTAAATAAAAAAAAACAATATGAGCAGCAAGTTGAA
AGTTTAAGAAACCAGTCATTCAATATGGAACAAGTTAATTATGTGAATCAGATGATGAAA
GATACTCAAGCAACTGTTGTCGCAATGAAAGATGGAATGAAATCGATGAAAAAAGAGTTT
AAAAAGATTAACATTGAAGATATTGAAGATCTTCAAGATGATATGACTGATATGCTTGAA
CAAGCAGATGAAGTCCAAAAAGCTCTTGGAAGAGATTATAACATGCCTGAAATTGATGAA
GATGTTCTGCAAGCAGAACTTGATGCATTGGGTGATGAATTTGTATTAGATGATGATAGC
AGTTATTTGAATGATATTATTAAAGCACCAGGTATTCCAGATAAAGAACCTGGAGCTAAT
AGCGTTGTTGCACCATCTTCAAAAACAAAGGATGGAGTTTTAGTCGATGAATTTGGTTTA
CCACAACTACCTGCAGCTTCATCATCTAAACAAAACTAA
>g6276.t1 Gene=g6276 Length=232
MHRLFGRGKPKKPPPNLNECIGKVDSRVEGIEKKIQILDNKLRKYKDQMAKIKEGPSMNA
LKQKALCVLNKKKQYEQQVESLRNQSFNMEQVNYVNQMMKDTQATVVAMKDGMKSMKKEF
KKINIEDIEDLQDDMTDMLEQADEVQKALGRDYNMPEIDEDVLQAELDALGDEFVLDDDS
SYLNDIIKAPGIPDKEPGANSVVAPSSKTKDGVLVDEFGLPQLPAASSSKQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6276.t1 | Coils | Coil | Coil | 28 | 55 | - |
| 7 | g6276.t1 | Coils | Coil | Coil | 58 | 92 | - |
| 5 | g6276.t1 | Coils | Coil | Coil | 128 | 148 | - |
| 4 | g6276.t1 | Gene3D | G3DSA:1.10.287.1060 | - | 16 | 95 | 8.5E-6 |
| 2 | g6276.t1 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 1 | 223 | 7.0E-74 |
| 3 | g6276.t1 | PANTHER | PTHR22761:SF69 | CHARGED MULTIVESICULAR BODY PROTEIN 5 | 1 | 223 | 7.0E-74 |
| 1 | g6276.t1 | Pfam | PF03357 | Snf7 | 13 | 196 | 5.2E-43 |
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.
