Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Charged multivesicular body protein 7.

Parent gene

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.t2 TTS g13427.t2 30000723 30000723
chr_1 g13427 g13427.t2 isoform g13427.t2 30000772 30002163
chr_1 g13427 g13427.t2 exon g13427.t2.exon1 30000772 30002163
chr_1 g13427 g13427.t2 cds g13427.t2.CDS1 30000857 30002146
chr_1 g13427 g13427.t2 TSS g13427.t2 30002363 30002363

Sequences

>g13427.t2 Gene=g13427 Length=1392
ATCGATGGGAAGATGACATGTTTATGTCTTCAATCATGTATAATTTTCGACCAAAGGAAG
TCAATCCAGAATATTATGAGCAAAAAATGCAGTTTTGGAAAGATATGATAGAATTATATT
GCGATTATAAAGGAAGTTGTTCAATTTCAATAAATGAACTAAAAGATGTCTTTAGAAGAA
AAGGAACATCACCGTACTGCTTATCGGATGTACTTAATCAAATGCAAAGCGAAGGAAACC
TTCAGGATAAGATTTCATTTATGCAGAAACCAAATGAAAGTTGGACTTCATGGACGATAA
ATACTTTTATATATAAACCTGCCAATTGGGGATTTTCAAAAATAAAAGAAAAAGTTATTG
GTGCCGGAAATCAATCAGATGATACAGTTTTTATTGTGAAAAGTGCAGTTCAGAAGCAAG
CTAGATTATTACAAGAACATGTAAAAAAACAACACAGCTATAATAACATTATTTCAATGG
ATGATTTAATGAAACATGCCGATGATATTGAAGGACTGTCTCGTGAAGGAATTTTCTTTG
CATTACAATATATGAGTGTTTATACAAAAACTGCCTACATCGAAGAACATCAAACAGCAG
GAGAAAATCATCATCATAAATTGCTTGTCAAATTCTCAGAACCGCATAAAAGTGTAGAAC
CAATTAAAGAGCTTGAACGATCAATTTACAATTTAGAGCACACAGAGAGATTTTTAATAG
AAACAATTGAAAAGAAAGAGTCATATTTGAATAGTGTTTTGAGTGATGTAAAAAATTGTC
TCAAAGATGGCAAGAAGCAAATGGCAAAAACATATCTTCGCAAAAAACATTTACTTGAGT
CAGATATTAACAAAACGATGAGCATACTCGATAACGTACAAGCAATGCTTCAACGAATTC
ATAATTCAAAGAGTGATAAGGAAATTTTAAGTGCCTACAAAATGGGATCTGATTCAATTA
AAAATACATTTGTCAAGTCAGGAATTAATATTGATAATGTACAAGACATTATTGAAGACA
TGCGTGAAGTAATTGAGGATCAAGATGAGTATGAAAATATTTTGAGTTCACCTATTCGAG
GTTTAAATGACATCGATGATTCTGAACTTGAAAAAGAATTGAATGATATCATAAATGAAA
ACAAGAAGCCTGGACCTAAAGATGACAAGAGCAATAAAGCAGTTGAAGATTTGAATTTGT
TGGACCTTGAAATGCGATTAAAAAGACTACGTTCGGATTTGCCTGATTTAGATGATGAGA
CCACATCAACCACTGTTCCTCGAAGTCACGAGAAATTCACTCAATAACTTTTTTTGTGTT
TTTATTATTTTTTTTGTATTAAAAATGTATGTAATTATAATGAAGGATGATGATGATGAA
GCATATATGCCT

>g13427.t2 Gene=g13427 Length=429
MFMSSIMYNFRPKEVNPEYYEQKMQFWKDMIELYCDYKGSCSISINELKDVFRRKGTSPY
CLSDVLNQMQSEGNLQDKISFMQKPNESWTSWTINTFIYKPANWGFSKIKEKVIGAGNQS
DDTVFIVKSAVQKQARLLQEHVKKQHSYNNIISMDDLMKHADDIEGLSREGIFFALQYMS
VYTKTAYIEEHQTAGENHHHKLLVKFSEPHKSVEPIKELERSIYNLEHTERFLIETIEKK
ESYLNSVLSDVKNCLKDGKKQMAKTYLRKKHLLESDINKTMSILDNVQAMLQRIHNSKSD
KEILSAYKMGSDSIKNTFVKSGINIDNVQDIIEDMREVIEDQDEYENILSSPIRGLNDID
DSELEKELNDIINENKKPGPKDDKSNKAVEDLNLLDLEMRLKRLRSDLPDLDDETTSTTV
PRSHEKFTQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g13427.t2 Coils Coil Coil 394 414 -
4 g13427.t2 MobiDBLite mobidb-lite consensus disorder prediction 406 429 -
2 g13427.t2 PANTHER PTHR22761 CHARGED MULTIVESICULAR BODY PROTEIN 148 388 6.5E-43
3 g13427.t2 PANTHER PTHR22761:SF46 PROTEIN CBG03253 148 388 6.5E-43
1 g13427.t2 Pfam PF03357 Snf7 215 377 1.9E-24

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0007034 vacuolar transport BP

KEGG

Orthology

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.

Raw TPM values