Gene loci information

Transcript annotation

  • This transcript has been annotated as Vesicle-fusing ATPase 1.

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 g7985 g7985.t5 isoform g7985.t5 27474402 27475565
chr_2 g7985 g7985.t5 exon g7985.t5.exon1 27474402 27474408
chr_2 g7985 g7985.t5 cds g7985.t5.CDS1 27474404 27474408
chr_2 g7985 g7985.t5 exon g7985.t5.exon2 27474469 27474594
chr_2 g7985 g7985.t5 cds g7985.t5.CDS2 27474469 27474594
chr_2 g7985 g7985.t5 exon g7985.t5.exon3 27474654 27474712
chr_2 g7985 g7985.t5 cds g7985.t5.CDS3 27474654 27474712
chr_2 g7985 g7985.t5 exon g7985.t5.exon4 27474776 27475060
chr_2 g7985 g7985.t5 cds g7985.t5.CDS4 27474776 27475060
chr_2 g7985 g7985.t5 exon g7985.t5.exon5 27475120 27475214
chr_2 g7985 g7985.t5 cds g7985.t5.CDS5 27475120 27475214
chr_2 g7985 g7985.t5 exon g7985.t5.exon6 27475280 27475498
chr_2 g7985 g7985.t5 cds g7985.t5.CDS6 27475280 27475498
chr_2 g7985 g7985.t5 exon g7985.t5.exon7 27475557 27475565
chr_2 g7985 g7985.t5 cds g7985.t5.CDS7 27475557 27475565
chr_2 g7985 g7985.t5 TSS g7985.t5 27475663 27475663
chr_2 g7985 g7985.t5 TTS g7985.t5 NA NA

Sequences

>g7985.t5 Gene=g7985 Length=800
ATGTCAGTTCGAATGAAAGCCACAAAGTGTCCAACTGACGAGCTCTCGTTGAAAAATCGA
GCAATAGTACATCCATCAGATTTTGGAAACAACGAAAATTATGTTGACGTTTCAACTGGT
CCAGGTCAACATTTTATTTTTGCAATTGAAAGGAGTGTTGAAGTTCCACCAAAATTTGTT
GGCTTTTCACTTTTGCAAAGAAAATGGGCTACACTCTCCATTAATCAAGATATTGATGTC
AAACCGTTCCGTTTTGAAGGATCTGGAAATGAACATGTTGTTTGTAATGTTTCATTAGAA
GTTGACTTTTTACAGAAGAAAACCATAACTCAAGAACCCTATGATTCAGATTTGATGGCA
AAAGAATTTCTTATGCAATTTGCTGGTTTAGCATTGACGGTCGGTCAACCTTTGGTCTTC
AGTTTCATGGATAAGAAACTCTTAGGCTTGAATATCAAGTCAATTGAGGCTATTGATGCT
TCATCTATTCGTGATAATAAAAATGCCGAGCCAAGAAAAATCAATTTTGGACGCCTTACA
GGCAATGCAGTCATTCAATTTGAGAAAGCTGAAAATTCTTCTCTTAATTTAGTTGGAAAG
GCAAAAGGAAAAGTTGTAAGGCAATCAATAATCAACCCTGATTGGGACTTTGGAAAAATG
GGAATTGGTGGTTTGGATAAAGAGTTCAATGCTATTTTCCGAAGAGCTTTTGCTTCACGA
GTTTTTCCACCAGAAGTAATTGAGCAACTCGGGTGCAAACATGTCAAAGGCATATTGCTT
TATGGTCCTCCAGGCACTGG

>g7985.t5 Gene=g7985 Length=266
MSVRMKATKCPTDELSLKNRAIVHPSDFGNNENYVDVSTGPGQHFIFAIERSVEVPPKFV
GFSLLQRKWATLSINQDIDVKPFRFEGSGNEHVVCNVSLEVDFLQKKTITQEPYDSDLMA
KEFLMQFAGLALTVGQPLVFSFMDKKLLGLNIKSIEAIDASSIRDNKNAEPRKINFGRLT
GNAVIQFEKAENSSLNLVGKAKGKVVRQSIINPDWDFGKMGIGGLDKEFNAIFRRAFASR
VFPPEVIEQLGCKHVKGILLYGPPGT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g7985.t5 Gene3D G3DSA:2.40.40.20 - 2 83 0.0e+00
9 g7985.t5 Gene3D G3DSA:3.10.330.10 - 87 197 0.0e+00
3 g7985.t5 PANTHER PTHR23078 VESICULAR-FUSION PROTEIN NSF 5 266 0.0e+00
4 g7985.t5 PANTHER PTHR23078:SF3 VESICLE-FUSING ATPASE 5 266 0.0e+00
2 g7985.t5 Pfam PF02359 Cell division protein 48 (CDC48), N-terminal domain 4 83 0.0e+00
1 g7985.t5 Pfam PF02933 Cell division protein 48 (CDC48), domain 2 113 166 2.0e-07
7 g7985.t5 SMART SM01073 CDC48_N_2 4 86 0.0e+00
8 g7985.t5 SMART SM01072 CDC48_2_2 113 185 4.2e-04
5 g7985.t5 SUPERFAMILY SSF50692 ADC-like 3 86 0.0e+00
6 g7985.t5 SUPERFAMILY SSF54585 Cdc48 domain 2-like 89 202 0.0e+00

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:0035494 SNARE complex disassembly BP
GO:0016887 ATP hydrolysis activity MF

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.

Raw TPM values