Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Charged multivesicular body protein 4a.

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_2 g7575 g7575.t6 isoform g7575.t6 24609592 24611309
chr_2 g7575 g7575.t6 exon g7575.t6.exon1 24609592 24610307
chr_2 g7575 g7575.t6 TTS g7575.t6 24609622 24609622
chr_2 g7575 g7575.t6 cds g7575.t6.CDS1 24610253 24610307
chr_2 g7575 g7575.t6 exon g7575.t6.exon2 24610525 24610891
chr_2 g7575 g7575.t6 cds g7575.t6.CDS2 24610525 24610891
chr_2 g7575 g7575.t6 exon g7575.t6.exon3 24611132 24611309
chr_2 g7575 g7575.t6 cds g7575.t6.CDS3 24611132 24611309
chr_2 g7575 g7575.t6 TSS g7575.t6 24611447 24611447

Sequences

>g7575.t6 Gene=g7575 Length=1261
ATGTCTTTTTTCAAGAATTTATTCGGCAAAAAAGAGCCTCCAGCTCCTTCGACTTCAGAG
AGTATTCAGAAATTGCGTGATACGGAAAATATGTTGTTAAAAAAACAAGAATTTTTAGAG
CAAAAGGTAGAACAAGAGCATGAAATAGCAAAAAAGAATGCTTCGACAAACAAAAGAGTC
GCACTACAAGCCTTAAAGAGGAAGAAGAGATACGAACAGCAATTAGAACAACTTCAGGGA
ACATTGACAACAATTGAGACTCAACGAGAGGCATTAGAGAACGCTAACACGAATGCAGCC
GTCCTCGATACAATGAAAGGAGCTTCAGATGCGCTCAAGAAAACGCATAAGGATATGAAT
ATTGATAATGTACATGATATGATGGATGACATTGCAGAACAAAATGATGTTGCAAATGAG
ATTTCAAACGCAATTTCCACTGGTATTATTTCACCTGGTGTTGATGAGGATGAGCTTGCA
AAGGAATTAGAAGAGTTGGAACAAGAAGGACTAGATTCAGAATTATTAAATGTTGGCCCG
GCGCCAAGCTTTCGACAGCTGATGCCTCATATTTTTCCAAAAAAATATAATATTGAATAA
TAATTATTTAATCCCAAAAAACAGCAAAAAAATTCAATGAAACATAAAAATTTTCAATAA
TTGTAATCTTTGTATTCTATGTTGCATCATCAAACATTATTTAAGGAAATAGTTGTGTTG
CATATTATACAAATATTACGCTTCTTTTATACTTTTAACTATGCATATTCATTAAAAATT
GGAATAGTTTTGTTCTATTCTTTGTGTCTGAACTTATTTTTTTTTCTTTTCATCGTCGTG
CTGCTTGAAGAAGGAAAGCGAATGTAGAGAAATGTGATTGAGGTGAAGTGTGTTGATTAT
TTGATTGTGCCGGATATTCAACTATATAGTTGTGTAGCATAACTTCAAATTTTCAACCTA
ATAAACCAGAAAATAAGTTAATATTAAGTATAACAATTTATAAAGAAGACAGAAGAAGAA
ATGAATAATGGTTTCGAGATTTTTTCTCTTGAGAAAAAAATGAGTCATCGACAAAAAATA
ATACTAACTGAGAACATCATCAACCTATGACGATTTTTGTATTTTATTTTACCTGAAAAG
TTTTAAATTTCATTTATTTGTTATATAGAAGCACTTTGATGAAACAAAAGAATTATTTCT
AATCAATTTGAATAAAAAGTTTAAAGAAATCATATTTTCTTTCTATTCATCTATTTCTTT
G

>g7575.t6 Gene=g7575 Length=199
MSFFKNLFGKKEPPAPSTSESIQKLRDTENMLLKKQEFLEQKVEQEHEIAKKNASTNKRV
ALQALKRKKRYEQQLEQLQGTLTTIETQREALENANTNAAVLDTMKGASDALKKTHKDMN
IDNVHDMMDDIAEQNDVANEISNAISTGIISPGVDEDELAKELEELEQEGLDSELLNVGP
APSFRQLMPHIFPKKYNIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7575.t6 Coils Coil Coil 22 42 -
6 g7575.t6 Coils Coil Coil 61 95 -
5 g7575.t6 Gene3D G3DSA:1.10.287.1060 - 16 93 1.5E-32
4 g7575.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
2 g7575.t6 PANTHER PTHR22761 CHARGED MULTIVESICULAR BODY PROTEIN 8 179 3.6E-75
3 g7575.t6 PANTHER PTHR22761:SF14 CHARGED MULTIVESICULAR BODY PROTEIN 4A 8 179 3.6E-75
1 g7575.t6 Pfam PF03357 Snf7 20 182 7.3E-49

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed