General information for g7575.t1
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.t1 | TTS | g7575.t1 | 24610208 | 24610208 |
| chr_2 | g7575 | g7575.t1 | isoform | g7575.t1 | 24610323 | 24611309 |
| chr_2 | g7575 | g7575.t1 | exon | g7575.t1.exon1 | 24610323 | 24610390 |
| chr_2 | g7575 | g7575.t1 | cds | g7575.t1.CDS1 | 24610323 | 24610390 |
| chr_2 | g7575 | g7575.t1 | exon | g7575.t1.exon2 | 24610457 | 24610891 |
| chr_2 | g7575 | g7575.t1 | cds | g7575.t1.CDS2 | 24610457 | 24610891 |
| chr_2 | g7575 | g7575.t1 | exon | g7575.t1.exon3 | 24611132 | 24611309 |
| chr_2 | g7575 | g7575.t1 | cds | g7575.t1.CDS3 | 24611132 | 24611309 |
| chr_2 | g7575 | g7575.t1 | TSS | g7575.t1 | 24611447 | 24611447 |
Sequences
>g7575.t1 Gene=g7575 Length=681
ATGTCTTTTTTCAAGAATTTATTCGGCAAAAAAGAGCCTCCAGCTCCTTCGACTTCAGAG
AGTATTCAGAAATTGCGTGATACGGAAAATATGTTGTTAAAAAAACAAGAATTTTTAGAG
CAAAAGGTAGAACAAGAGCATGAAATAGCAAAAAAGAATGCTTCGACAAACAAAAGAGTC
GCACTACAAGCCTTAAAGAGGAAGAAGAGATACGAACAGCAATTAGAACAACTTCAGGGA
ACATTGACAACAATTGAGACTCAACGAGAGGCATTAGAGAACGCTAACACGAATGCAGCC
GTCCTCGATACAATGAAAGGAGCTTCAGATGCGCTCAAGAAAACGCATAAGGATATGAAT
ATTGATAATGTACATGATATGATGGATGACATTGCAGAACAAAATGATGTTGCAAATGAG
ATTTCAAACGCAATTTCCACTGGTATTATTTCACCTGGTGTTGATGAGGATGAGCTTGCA
AAGGAATTAGAAGAGTTGGAACAAGAAGGACTAGATTCAGAATTATTAAATGTTGGCCCG
GCGCCGAACAAACTCCCCGAAGTTCCAAGCACAGATTTACCGACAGCTTCGAAGGACAAA
GAAAAGAAAAAAGCAAAACCAGTCGCTGCAGATGAAGACGATGATCCAGATATGAAGGAA
TTAATGCAATGGGCTAATTAA
>g7575.t1 Gene=g7575 Length=226
MSFFKNLFGKKEPPAPSTSESIQKLRDTENMLLKKQEFLEQKVEQEHEIAKKNASTNKRV
ALQALKRKKRYEQQLEQLQGTLTTIETQREALENANTNAAVLDTMKGASDALKKTHKDMN
IDNVHDMMDDIAEQNDVANEISNAISTGIISPGVDEDELAKELEELEQEGLDSELLNVGP
APNKLPEVPSTDLPTASKDKEKKKAKPVAADEDDDPDMKELMQWAN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7575.t1 | Coils | Coil | Coil | 22 | 42 | - |
| 8 | g7575.t1 | Coils | Coil | Coil | 61 | 95 | - |
| 7 | g7575.t1 | Gene3D | G3DSA:1.10.287.1060 | - | 16 | 93 | 2.0E-32 |
| 5 | g7575.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 4 | g7575.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 176 | 226 | - |
| 6 | g7575.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 213 | - |
| 2 | g7575.t1 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 8 | 222 | 5.6E-80 |
| 3 | g7575.t1 | PANTHER | PTHR22761:SF14 | CHARGED MULTIVESICULAR BODY PROTEIN 4A | 8 | 222 | 5.6E-80 |
| 1 | g7575.t1 | Pfam | PF03357 | Snf7 | 20 | 192 | 1.2E-51 |
| 10 | g7575.t1 | ProSiteProfiles | PS51179 | POU-specific (POUs) domain profile. | 213 | 226 | 8.758 |
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:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0007034 | vacuolar transport | BP |
| GO:0003700 | DNA-binding transcription factor activity | MF |
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.
