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.t8 TTS g7575.t8 24610208 24610208
chr_2 g7575 g7575.t8 isoform g7575.t8 24610323 24611309
chr_2 g7575 g7575.t8 exon g7575.t8.exon1 24610323 24610381
chr_2 g7575 g7575.t8 cds g7575.t8.CDS1 24610323 24610381
chr_2 g7575 g7575.t8 exon g7575.t8.exon2 24610457 24610879
chr_2 g7575 g7575.t8 cds g7575.t8.CDS2 24610457 24610879
chr_2 g7575 g7575.t8 exon g7575.t8.exon3 24611132 24611309
chr_2 g7575 g7575.t8 cds g7575.t8.CDS3 24611132 24611309
chr_2 g7575 g7575.t8 TSS g7575.t8 24611447 24611447

Sequences

>g7575.t8 Gene=g7575 Length=660
ATGTCTTTTTTCAAGAATTTATTCGGCAAAAAAGAGCCTCCAGCTCCTTCGACTTCAGAG
AGTATTCAGAAATTGCGTGATACGGAAAATATGTTGTTAAAAAAACAAGAATTTTTAGAG
CAAAAGGTAGAACAAGAGCATGAAATAGCAAAAAAGAATGCTTCGACAAACAAAAGAGCC
TTAAAGAGGAAGAAGAGATACGAACAGCAATTAGAACAACTTCAGGGAACATTGACAACA
ATTGAGACTCAACGAGAGGCATTAGAGAACGCTAACACGAATGCAGCCGTCCTCGATACA
ATGAAAGGAGCTTCAGATGCGCTCAAGAAAACGCATAAGGATATGAATATTGATAATGTA
CATGATATGATGGATGACATTGCAGAACAAAATGATGTTGCAAATGAGATTTCAAACGCA
ATTTCCACTGGTATTATTTCACCTGGTGTTGATGAGGATGAGCTTGCAAAGGAATTAGAA
GAGTTGGAACAAGAAGGACTAGATTCAGAATTATTAAATGTTGGCCCGGCGCCGAACAAA
CTCCCCGAAGTTCCAAGCACAGATTTACCGACAGCTTCGAAGGACAAAGAAAAGAAAAAA
GTCGCTGCAGATGAAGACGATGATCCAGATATGAAGGAATTAATGCAATGGGCTAATTAA

>g7575.t8 Gene=g7575 Length=219
MSFFKNLFGKKEPPAPSTSESIQKLRDTENMLLKKQEFLEQKVEQEHEIAKKNASTNKRA
LKRKKRYEQQLEQLQGTLTTIETQREALENANTNAAVLDTMKGASDALKKTHKDMNIDNV
HDMMDDIAEQNDVANEISNAISTGIISPGVDEDELAKELEELEQEGLDSELLNVGPAPNK
LPEVPSTDLPTASKDKEKKKVAADEDDDPDMKELMQWAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7575.t8 Coils Coil Coil 22 42 -
8 g7575.t8 Coils Coil Coil 57 91 -
7 g7575.t8 Gene3D G3DSA:1.10.287.1060 - 16 89 8.9E-27
5 g7575.t8 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
4 g7575.t8 MobiDBLite mobidb-lite consensus disorder prediction 165 219 -
6 g7575.t8 MobiDBLite mobidb-lite consensus disorder prediction 190 207 -
2 g7575.t8 PANTHER PTHR22761 CHARGED MULTIVESICULAR BODY PROTEIN 8 215 2.2E-74
3 g7575.t8 PANTHER PTHR22761:SF14 CHARGED MULTIVESICULAR BODY PROTEIN 4A 8 215 2.2E-74
1 g7575.t8 Pfam PF03357 Snf7 20 188 8.1E-47
10 g7575.t8 ProSiteProfiles PS51179 POU-specific (POUs) domain profile. 206 219 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

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. There were no conditions that were differentially expressed