General information for g7575.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Charged multivesicular body protein 4a.
Parent gene
- The parent gene g7575 is located on chr_2: 24611131..24611309 (- 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 | g7575 | g7575.t11 | isoform | g7575.t11 | 24610457 | 24611309 |
| chr_2 | g7575 | g7575.t11 | exon | g7575.t11.exon1 | 24610457 | 24610891 |
| chr_2 | g7575 | g7575.t11 | cds | g7575.t11.CDS1 | 24610458 | 24610891 |
| chr_2 | g7575 | g7575.t11 | TTS | g7575.t11 | 24610473 | 24610473 |
| chr_2 | g7575 | g7575.t11 | exon | g7575.t11.exon2 | 24611132 | 24611309 |
| chr_2 | g7575 | g7575.t11 | cds | g7575.t11.CDS2 | 24611132 | 24611309 |
| chr_2 | g7575 | g7575.t11 | TSS | g7575.t11 | 24611447 | 24611447 |
Sequences
>g7575.t11 Gene=g7575 Length=613
ATGTCTTTTTTCAAGAATTTATTCGGCAAAAAAGAGCCTCCAGCTCCTTCGACTTCAGAG
AGTATTCAGAAATTGCGTGATACGGAAAATATGTTGTTAAAAAAACAAGAATTTTTAGAG
CAAAAGGTAGAACAAGAGCATGAAATAGCAAAAAAGAATGCTTCGACAAACAAAAGAGTC
GCACTACAAGCCTTAAAGAGGAAGAAGAGATACGAACAGCAATTAGAACAACTTCAGGGA
ACATTGACAACAATTGAGACTCAACGAGAGGCATTAGAGAACGCTAACACGAATGCAGCC
GTCCTCGATACAATGAAAGGAGCTTCAGATGCGCTCAAGAAAACGCATAAGGATATGAAT
ATTGATAATGTACATGATATGATGGATGACATTGCAGAACAAAATGATGTTGCAAATGAG
ATTTCAAACGCAATTTCCACTGGTATTATTTCACCTGGTGTTGATGAGGATGAGCTTGCA
AAGGAATTAGAAGAGTTGGAACAAGAAGGACTAGATTCAGAATTATTAAATGTTGGCCCG
GCGCCGAACAAACTCCCCGAAGTTCCAAGCACAGATTTACCGACAGCTTCGAAGGACAAA
GAAAAGAAAAAAG
>g7575.t11 Gene=g7575 Length=204
MSFFKNLFGKKEPPAPSTSESIQKLRDTENMLLKKQEFLEQKVEQEHEIAKKNASTNKRV
ALQALKRKKRYEQQLEQLQGTLTTIETQREALENANTNAAVLDTMKGASDALKKTHKDMN
IDNVHDMMDDIAEQNDVANEISNAISTGIISPGVDEDELAKELEELEQEGLDSELLNVGP
APNKLPEVPSTDLPTASKDKEKKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7575.t11 | Coils | Coil | Coil | 22 | 42 | - |
| 7 | g7575.t11 | Coils | Coil | Coil | 61 | 95 | - |
| 6 | g7575.t11 | Gene3D | G3DSA:1.10.287.1060 | - | 16 | 93 | 1.6E-32 |
| 4 | g7575.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 5 | g7575.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 171 | 204 | - |
| 2 | g7575.t11 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 8 | 195 | 2.4E-80 |
| 3 | g7575.t11 | PANTHER | PTHR22761:SF14 | CHARGED MULTIVESICULAR BODY PROTEIN 4A | 8 | 195 | 2.4E-80 |
| 1 | g7575.t11 | Pfam | PF03357 | Snf7 | 20 | 192 | 8.3E-52 |
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 K12194 (charged multivesicular body protein 4A/B)
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.
