General information for g11340.t9
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.t9 | TTS | g11340.t9 | 15727669 | 15727669 |
| chr_1 | g11340 | g11340.t9 | isoform | g11340.t9 | 15727827 | 15728593 |
| chr_1 | g11340 | g11340.t9 | exon | g11340.t9.exon1 | 15727827 | 15728405 |
| chr_1 | g11340 | g11340.t9 | cds | g11340.t9.CDS1 | 15727827 | 15728405 |
| chr_1 | g11340 | g11340.t9 | exon | g11340.t9.exon2 | 15728543 | 15728593 |
| chr_1 | g11340 | g11340.t9 | cds | g11340.t9.CDS2 | 15728543 | 15728593 |
| chr_1 | g11340 | g11340.t9 | TSS | g11340.t9 | 15728694 | 15728694 |
Sequences
>g11340.t9 Gene=g11340 Length=630
ATGGAGTGGCTTTTTGGTAAAAAGATGACACCCGATGAAATGCTTAGAAAGGAAAAGAAA
GTCATTGCTGATATTAAAAAACTTGCAAAAGAAAATCAAATGGATGCAGTAAAAATAATG
GCAAAGGATCTTGTGCGAACCAGAAGGCAAGTTAGAAAATTTATGTTGATGAAGGCAAAC
ATCCAGGCAGTTTCTCTCAAAATTCAAACACTCAAATCACAAAACACAATGGCTCAAGCT
ATGAAAGGTGTGAGTCGTGCAATGATGAATATGAATAGACAAATGAATATGCCACAGATA
CAACAAATTCTTCATGAATTCGAAAAACAATCTGAAATAATGGACATGAAAGAAGAAATG
ATTAATGATGTTATTGATGATGCAATGGAAGATGAGGGAGATGAGGAAGAAACTGACGCC
GTTGTGTCACAAGTTTTAGATGAATTAGGTCTCCAATTAAATGATCAGCTATCAGGACTA
CCGCAAGCATCTGGATCACTTTCCGTCGTTGGTCAAAAACAACCTCAGGCAGCTGCTGTT
GCTGCTGGTGGTGGAGCTGCCGCTGGTGGCAATTCACCCGATGCTGATGATGAACTTCAA
AAGCGCCTTGATAATTTGCGTCGAGAATAA
>g11340.t9 Gene=g11340 Length=209
MEWLFGKKMTPDEMLRKEKKVIADIKKLAKENQMDAVKIMAKDLVRTRRQVRKFMLMKAN
IQAVSLKIQTLKSQNTMAQAMKGVSRAMMNMNRQMNMPQIQQILHEFEKQSEIMDMKEEM
INDVIDDAMEDEGDEEETDAVVSQVLDELGLQLNDQLSGLPQASGSLSVVGQKQPQAAAV
AAGGGAAAGGNSPDADDELQKRLDNLRRE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g11340.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 181 | 209 | - |
| 5 | g11340.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 195 | 209 | - |
| 2 | g11340.t9 | PANTHER | PTHR10476:SF4 | CHARGED MULTIVESICULAR BODY PROTEIN 2A | 12 | 208 | 8.3E-68 |
| 3 | g11340.t9 | PANTHER | PTHR10476 | CHARGED MULTIVESICULAR BODY PROTEIN | 12 | 208 | 8.3E-68 |
| 1 | g11340.t9 | Pfam | PF03357 | Snf7 | 13 | 163 | 8.3E-36 |
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.
