Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vacuolar protein sorting-associated protein 45.

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_3 g4087 g4087.t20 isoform g4087.t20 30512084 30513633
chr_3 g4087 g4087.t20 exon g4087.t20.exon1 30512084 30512397
chr_3 g4087 g4087.t20 cds g4087.t20.CDS1 30512084 30512397
chr_3 g4087 g4087.t20 exon g4087.t20.exon2 30512457 30512606
chr_3 g4087 g4087.t20 cds g4087.t20.CDS2 30512457 30512466
chr_3 g4087 g4087.t20 exon g4087.t20.exon3 30512688 30513510
chr_3 g4087 g4087.t20 exon g4087.t20.exon4 30513568 30513633
chr_3 g4087 g4087.t20 TTS g4087.t20 30514294 30514294
chr_3 g4087 g4087.t20 TSS g4087.t20 NA NA

Sequences

>g4087.t20 Gene=g4087 Length=1353
GTTTGTGTATTGAAAGAGTTGCTTGAAGAAATTTTTAAAGGTCGACCAATTGATCAACAA
TATCCATTTATTAATTCATCAGAAGTTCCTTATAGGCGACCACCGACAGAAATTATTGTT
TTTATAGTTGGTGGTGCCACATATGAAGAAGCTTTGGCAGTTCATCAACTTAATCAATTG
GGTTATCGTGTTATATTAGGAGGCACAACTATTCATAATTCTGAAACTTTCCTAGAAGAA
GTTATTGCAGCAACAAATGGAGCACCTTTTAAACATTCCCGATCACTGCAAGCTTTTCAT
AATGCATCAAATGCCAATTATTAATTTATTATAATAAAATATATAACCAAAACTATAAAT
GAATTGATGTATTCACTACTCATCGTCATTATCTGTGTAGTCATTAAAATCACTGAATGA
TGTCTCGGGTTCATTCAGTCTCAATTTTTCAGCTATAACAATCTAATATTCCACTAAAAT
ATCCATATCCAAACATTGCAATTGAAGCAATTAAACCTGACATGATGTATCTTTTTCTAA
TTTCTGACGGTGGATCTTCATCTTCTTGCCCAGTAAAAACTTTTTGTTCTTTCTTTAGAT
TTTGTGCCTTTACTTTTTCACTCTCAAAGCACTCATTTTCATTAAAGAACTTTTTCTTTA
AATTATCCACATAACGTGATAGATTTTTACATTGATTAGCATGTGATTGAAGTTGATTAT
TTGGTAATTGAAATTTAAGTATAATTGCTAAATAAGCAAAAATAGTTGCATCAACTTCAT
TTTGTGATCCATTAATGAAGAATTCTTTATTTCCCAGTCGTTCGCTTATCCAATTAAGAC
ATTTTTTTGCATCCACTTCCATTTTCGTTGTATCATGTGCAGTAACTGGGTCTTCTAGTG
AAAAATTAGCTACATTTTGACATACTTGTTCACATTTCCGCACATATTTTGAAGGATAAT
AAAAATTAAATGGAAATGGTGTTCTAAGTGCATAAAGCGCTCTAGTCTCATCGATATTTT
GAGGATTTCCAAATAATTGATACATTAGAAAAGGATAAAGATTTTGAGTAATATACATAA
TGTAAGCTTCATTTTTCTCTGATCCATCAAGTGTGTAACCTTCTTTCTTTAAAAAATTGA
TAATTCTCTCATAGCCACAATACTTTTTGTTATCGCTTGAATCTATTAAGTAAGGTAGAA
AACCATTATTTGAATGAAAGGGTGAACAATCAGTCCTTATTTTAATTCCTTGTATGTCTG
CTAGTTTTATGTACATCTTAAAAAAAAAACTCTCAAACAATCGAGATCTATTGAAGGCAA
TTGATATTCTCCTTTATAAACAAATAGCTCCAT

>g4087.t20 Gene=g4087 Length=107
VCVLKELLEEIFKGRPIDQQYPFINSSEVPYRRPPTEIIVFIVGGATYEEALAVHQLNQL
GYRVILGGTTIHNSETFLEEVIAATNGAPFKHSRSLQAFHNASNANY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g4087.t20 Gene3D G3DSA:3.40.50.1910 - 2 88 0
2 g4087.t20 PANTHER PTHR11679:SF3 VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 2 82 0
3 g4087.t20 PANTHER PTHR11679 VESICLE PROTEIN SORTING-ASSOCIATED 2 82 0
1 g4087.t20 Pfam PF00995 Sec1 family 4 80 0
4 g4087.t20 SUPERFAMILY SSF56815 Sec1/munc18-like (SM) proteins 3 86 0

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:0016192 vesicle-mediated 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.

Raw TPM values