General information for g11340.t11
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.t11 | TTS | g11340.t11 | 15727669 | 15727669 |
| chr_1 | g11340 | g11340.t11 | isoform | g11340.t11 | 15727827 | 15729758 |
| chr_1 | g11340 | g11340.t11 | exon | g11340.t11.exon1 | 15727827 | 15728471 |
| chr_1 | g11340 | g11340.t11 | cds | g11340.t11.CDS1 | 15727827 | 15728471 |
| chr_1 | g11340 | g11340.t11 | exon | g11340.t11.exon2 | 15728543 | 15728619 |
| chr_1 | g11340 | g11340.t11 | cds | g11340.t11.CDS2 | 15728543 | 15728619 |
| chr_1 | g11340 | g11340.t11 | exon | g11340.t11.exon3 | 15729752 | 15729758 |
| chr_1 | g11340 | g11340.t11 | cds | g11340.t11.CDS3 | 15729752 | 15729758 |
| chr_1 | g11340 | g11340.t11 | TSS | g11340.t11 | 15730161 | 15730161 |
Sequences
>g11340.t11 Gene=g11340 Length=729
ATGTTTCAATTAGGAAAAAGATTAATTTGCAAAATGGAGTGGCTTTTTGGTAAAAAGATG
ACACCCGATGAAATGCTTAGAAAGAATCAAAGAGCCTTGAACAAAGCAATGCGAGATCTT
GATCGAGAAAAAATGAAAATGGAACAACAGGAAAAGAAAGTCATTGCTGATATTAAAAAA
CTTGCAAAAGAAAATCAAATGGATGCAGTAAAAATAATGGCAAAGGATCTTGTGCGAACC
AGAAGGCAAGTTAGAAAATTTATGTTGATGAAGGCAAACATCCAGGCAGTTTCTCTCAAA
ATTCAAACACTCAAATCACAAAACACAATGGCTCAAGCTATGAAAGGTGTGAGTCGTGCA
ATGATGAATATGAATAGACAAATGAATATGCCACAGATACAACAAATTCTTCATGAATTC
GAAAAACAATCTGAAATAATGGACATGAAAGAAGAAATGATTAATGATGTTATTGATGAT
GCAATGGAAGATGAGGGAGATGAGGAAGAAACTGACGCCGTTGTGTCACAAGTTTTAGAT
GAATTAGGTCTCCAATTAAATGATCAGCTATCAGGACTACCGCAAGCATCTGGATCACTT
TCCGTCGTTGGTCAAAAACAACCTCAGGCAGCTGCTGTTGCTGCTGGTGGTGGAGCTGCC
GCTGGTGGCAATTCACCCGATGCTGATGATGAACTTCAAAAGCGCCTTGATAATTTGCGT
CGAGAATAA
>g11340.t11 Gene=g11340 Length=242
MFQLGKRLICKMEWLFGKKMTPDEMLRKNQRALNKAMRDLDREKMKMEQQEKKVIADIKK
LAKENQMDAVKIMAKDLVRTRRQVRKFMLMKANIQAVSLKIQTLKSQNTMAQAMKGVSRA
MMNMNRQMNMPQIQQILHEFEKQSEIMDMKEEMINDVIDDAMEDEGDEEETDAVVSQVLD
ELGLQLNDQLSGLPQASGSLSVVGQKQPQAAAVAAGGGAAAGGNSPDADDELQKRLDNLR
RE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11340.t11 | Coils | Coil | Coil | 26 | 64 | - |
| 4 | g11340.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 242 | - |
| 5 | g11340.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 228 | 242 | - |
| 2 | g11340.t11 | PANTHER | PTHR10476:SF4 | CHARGED MULTIVESICULAR BODY PROTEIN 2A | 12 | 241 | 6.8E-83 |
| 3 | g11340.t11 | PANTHER | PTHR10476 | CHARGED MULTIVESICULAR BODY PROTEIN | 12 | 241 | 6.8E-83 |
| 1 | g11340.t11 | Pfam | PF03357 | Snf7 | 29 | 196 | 1.2E-40 |
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 transcript has been annotated with K12191 (charged multivesicular body protein 2A)
Pathway
- This transcript belongs to the following pathways
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.
