General information for g11340.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Charged multivesicular body protein 2a.
Parent gene
- The parent gene g11340 is located on chr_1: 15727827..15729772 (- 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 | g11340 | g11340.t5 | isoform | g11340.t5 | 15727486 | 15728474 |
| chr_1 | g11340 | g11340.t5 | exon | g11340.t5.exon1 | 15727486 | 15728474 |
| chr_1 | g11340 | g11340.t5 | cds | g11340.t5.CDS1 | 15727827 | 15728447 |
| chr_1 | g11340 | g11340.t5 | TSS | g11340.t5 | 15728694 | 15728694 |
| chr_1 | g11340 | g11340.t5 | TTS | g11340.t5 | NA | NA |
Sequences
>g11340.t5 Gene=g11340 Length=989
AAGAATCAAAGAGCCTTGAACAAAGCAATGCGAGATCTTGATCGAGAAAAAATGAAAATG
GAACAACAGGAAAAGAAAGTCATTGCTGATATTAAAAAACTTGCAAAAGAAAATCAAATG
GATGCAGTAAAAATAATGGCAAAGGATCTTGTGCGAACCAGAAGGCAAGTTAGAAAATTT
ATGTTGATGAAGGCAAACATCCAGGCAGTTTCTCTCAAAATTCAAACACTCAAATCACAA
AACACAATGGCTCAAGCTATGAAAGGTGTGAGTCGTGCAATGATGAATATGAATAGACAA
ATGAATATGCCACAGATACAACAAATTCTTCATGAATTCGAAAAACAATCTGAAATAATG
GACATGAAAGAAGAAATGATTAATGATGTTATTGATGATGCAATGGAAGATGAGGGAGAT
GAGGAAGAAACTGACGCCGTTGTGTCACAAGTTTTAGATGAATTAGGTCTCCAATTAAAT
GATCAGCTATCAGGACTACCGCAAGCATCTGGATCACTTTCCGTCGTTGGTCAAAAACAA
CCTCAGGCAGCTGCTGTTGCTGCTGGTGGTGGAGCTGCCGCTGGTGGCAATTCACCCGAT
GCTGATGATGAACTTCAAAAGCGCCTTGATAATTTGCGTCGAGAATAATTATCTTACCGA
ATTTTGATTTCATTTTCATCAAGATGAATTTCGTTAAATTTTGATTTTTTTATCTAACTT
AACAATATTATTCAAATATACCACACATTTTAAACTATATTTTTTGAAAGAAGAATAAAT
TTTATTATTAAGTACTATGAATCAATAATTTCATATATGATACATTTCATTAATTTAAAA
ATAAATAAATAATTATGATACTTTGTGCTTCAGAATTTTTATAAAATATACAGCTTGCAA
TTAGAAAATATTGTTAATTAAGAAAAAAATTAACAACTTGTTCATTCTATTATAATAAGA
AGCAAAATTAGTCTAAAATCATATTTATT
>g11340.t5 Gene=g11340 Length=206
MRDLDREKMKMEQQEKKVIADIKKLAKENQMDAVKIMAKDLVRTRRQVRKFMLMKANIQA
VSLKIQTLKSQNTMAQAMKGVSRAMMNMNRQMNMPQIQQILHEFEKQSEIMDMKEEMIND
VIDDAMEDEGDEEETDAVVSQVLDELGLQLNDQLSGLPQASGSLSVVGQKQPQAAAVAAG
GGAAAGGNSPDADDELQKRLDNLRRE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11340.t5 | Coils | Coil | Coil | 1 | 28 | - |
| 4 | g11340.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 164 | 206 | - |
| 5 | g11340.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 192 | 206 | - |
| 2 | g11340.t5 | PANTHER | PTHR10476:SF4 | CHARGED MULTIVESICULAR BODY PROTEIN 2A | 1 | 205 | 4.1E-72 |
| 3 | g11340.t5 | PANTHER | PTHR10476 | CHARGED MULTIVESICULAR BODY PROTEIN | 1 | 205 | 4.1E-72 |
| 1 | g11340.t5 | Pfam | PF03357 | Snf7 | 1 | 160 | 4.5E-38 |
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.
