General information for g13427.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Charged multivesicular body protein 7.
Parent gene
- The parent gene g13427 is located on chr_1: 30000857..30002325 (- 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 | g13427 | g13427.t1 | TTS | g13427.t1 | 30000723 | 30000723 |
| chr_1 | g13427 | g13427.t1 | isoform | g13427.t1 | 30000857 | 30002325 |
| chr_1 | g13427 | g13427.t1 | exon | g13427.t1.exon1 | 30000857 | 30002163 |
| chr_1 | g13427 | g13427.t1 | cds | g13427.t1.CDS1 | 30000857 | 30002163 |
| chr_1 | g13427 | g13427.t1 | exon | g13427.t1.exon2 | 30002250 | 30002325 |
| chr_1 | g13427 | g13427.t1 | cds | g13427.t1.CDS2 | 30002250 | 30002325 |
| chr_1 | g13427 | g13427.t1 | TSS | g13427.t1 | 30002363 | 30002363 |
Sequences
>g13427.t1 Gene=g13427 Length=1383
ATGAATAAATCAAAAAACAACAGAAGATCGTTAGATACAAACAAACTTTATGTTCTCGAT
AAAGATTTCTATCCAGATCGATGGGAAGATGACATGTTTATGTCTTCAATCATGTATAAT
TTTCGACCAAAGGAAGTCAATCCAGAATATTATGAGCAAAAAATGCAGTTTTGGAAAGAT
ATGATAGAATTATATTGCGATTATAAAGGAAGTTGTTCAATTTCAATAAATGAACTAAAA
GATGTCTTTAGAAGAAAAGGAACATCACCGTACTGCTTATCGGATGTACTTAATCAAATG
CAAAGCGAAGGAAACCTTCAGGATAAGATTTCATTTATGCAGAAACCAAATGAAAGTTGG
ACTTCATGGACGATAAATACTTTTATATATAAACCTGCCAATTGGGGATTTTCAAAAATA
AAAGAAAAAGTTATTGGTGCCGGAAATCAATCAGATGATACAGTTTTTATTGTGAAAAGT
GCAGTTCAGAAGCAAGCTAGATTATTACAAGAACATGTAAAAAAACAACACAGCTATAAT
AACATTATTTCAATGGATGATTTAATGAAACATGCCGATGATATTGAAGGACTGTCTCGT
GAAGGAATTTTCTTTGCATTACAATATATGAGTGTTTATACAAAAACTGCCTACATCGAA
GAACATCAAACAGCAGGAGAAAATCATCATCATAAATTGCTTGTCAAATTCTCAGAACCG
CATAAAAGTGTAGAACCAATTAAAGAGCTTGAACGATCAATTTACAATTTAGAGCACACA
GAGAGATTTTTAATAGAAACAATTGAAAAGAAAGAGTCATATTTGAATAGTGTTTTGAGT
GATGTAAAAAATTGTCTCAAAGATGGCAAGAAGCAAATGGCAAAAACATATCTTCGCAAA
AAACATTTACTTGAGTCAGATATTAACAAAACGATGAGCATACTCGATAACGTACAAGCA
ATGCTTCAACGAATTCATAATTCAAAGAGTGATAAGGAAATTTTAAGTGCCTACAAAATG
GGATCTGATTCAATTAAAAATACATTTGTCAAGTCAGGAATTAATATTGATAATGTACAA
GACATTATTGAAGACATGCGTGAAGTAATTGAGGATCAAGATGAGTATGAAAATATTTTG
AGTTCACCTATTCGAGGTTTAAATGACATCGATGATTCTGAACTTGAAAAAGAATTGAAT
GATATCATAAATGAAAACAAGAAGCCTGGACCTAAAGATGACAAGAGCAATAAAGCAGTT
GAAGATTTGAATTTGTTGGACCTTGAAATGCGATTAAAAAGACTACGTTCGGATTTGCCT
GATTTAGATGATGAGACCACATCAACCACTGTTCCTCGAAGTCACGAGAAATTCACTCAA
TAA
>g13427.t1 Gene=g13427 Length=460
MNKSKNNRRSLDTNKLYVLDKDFYPDRWEDDMFMSSIMYNFRPKEVNPEYYEQKMQFWKD
MIELYCDYKGSCSISINELKDVFRRKGTSPYCLSDVLNQMQSEGNLQDKISFMQKPNESW
TSWTINTFIYKPANWGFSKIKEKVIGAGNQSDDTVFIVKSAVQKQARLLQEHVKKQHSYN
NIISMDDLMKHADDIEGLSREGIFFALQYMSVYTKTAYIEEHQTAGENHHHKLLVKFSEP
HKSVEPIKELERSIYNLEHTERFLIETIEKKESYLNSVLSDVKNCLKDGKKQMAKTYLRK
KHLLESDINKTMSILDNVQAMLQRIHNSKSDKEILSAYKMGSDSIKNTFVKSGINIDNVQ
DIIEDMREVIEDQDEYENILSSPIRGLNDIDDSELEKELNDIINENKKPGPKDDKSNKAV
EDLNLLDLEMRLKRLRSDLPDLDDETTSTTVPRSHEKFTQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13427.t1 | Coils | Coil | Coil | 425 | 445 | - |
| 4 | g13427.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 437 | 460 | - |
| 2 | g13427.t1 | PANTHER | PTHR22761 | CHARGED MULTIVESICULAR BODY PROTEIN | 175 | 419 | 2.1E-43 |
| 3 | g13427.t1 | PANTHER | PTHR22761:SF46 | PROTEIN CBG03253 | 175 | 419 | 2.1E-43 |
| 1 | g13427.t1 | Pfam | PF03357 | Snf7 | 246 | 408 | 2.2E-24 |
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 K15053 (charged multivesicular body protein 7)
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.
