Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vacuolar protein-sorting-associated protein 36.

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 g721 g721.t20 TTS g721.t20 5500769 5500769
chr_3 g721 g721.t20 isoform g721.t20 5501439 5503186
chr_3 g721 g721.t20 exon g721.t20.exon1 5501439 5501562
chr_3 g721 g721.t20 exon g721.t20.exon2 5501629 5502212
chr_3 g721 g721.t20 exon g721.t20.exon3 5502270 5502722
chr_3 g721 g721.t20 cds g721.t20.CDS1 5502618 5502722
chr_3 g721 g721.t20 exon g721.t20.exon4 5502783 5503186
chr_3 g721 g721.t20 cds g721.t20.CDS2 5502783 5503121
chr_3 g721 g721.t20 TSS g721.t20 5504057 5504057

Sequences

>g721.t20 Gene=g721 Length=1565
AGTATGTTTCTTATAATTTTTATTTATAATATAATATAAGTAAATCATTTTAGGAACAAG
GTGGTATGATGACAATAACTGAAGTTTATTGCCGAATAAATCGTGCTCGTGGTTTAGAAT
TGGTTTCACCAGAGGATGTTTTAAATGCTTGTAAATTACTCAATGGACCTATGAAATTAA
GACAATACCCTTCTGGTGCAATGATTCTTCAACTTGAAAATCACAATGATGATCAAGTTG
CTGAAGAAATTGAAAAGTTAGTAATTGAATCAGAATCAATGTCCATAGAAGAATGCGCAC
GATTAAAAAACATTAGTGTTCTTCTGGCTCATGAACGCTTCCTCATTTCTGAAAATGCTG
GAAAAATTTGTAGAGATGAATCTGTTGAAGGTCTTAGATTCTATATAATATTTAATGCTA
AGCATATACACTTTTTATTTCTCGGGCTCAAATGTTATCGTCAAATCTCCAAATTTGTGA
ATTGTTTCTTCATAAATGTCTTCAGGTAATTTTGACTCATCACCGAGAAAAGTTGGAAAA
TGAAGAGGTTCTTTAGGTTGACGAAGTGGTAAAACTGTATCATAAATATAAACTAAACTT
CCAGGTGCTCCTGCGATTGCTCTACCTGACACCCAAATACAATTTTCTTTTCTATTAATT
CTCCAAATTTTTAAACCACGAAGAGTTCTCCATCGATTCCCCATATTTCCAGGCATTTTC
TTTCCTTTCCAAATTCTACTTTTAATGCCTGAAGCCAAAGATCCTCCACGTCTATGATTT
TTAGTAGTTCCATGAGTTGCTGGTCCTCCTTTAAATCCCCATCTTTTAATGACACCTTGC
CAGCCTTGATCAACGCTTTACCCAATACATCAACATAATCACCAACACGATAATGAAGAG
CATTGATTGATGTGCCTATAGGAAGTGCTGCATCAGGATGTATGATAAAACGCGTAATTC
TTTGTGTTGGCATCACACCACTTTCTTTAAATAAACCCATGTAATTTGCTGTCAATCGGT
TTGGATCAGCTTCTCCTGATCCTATATAGAGACAACCTTTTTTATTGTAATTACCTAGAC
GTTTTCTCATTGTAGGATTGAATTCTCCAGGTGGTGCATATTTAATGACATGATTTTCAA
TGATTTGTAAAACTGTCGTACAAATTCGAGTACCATCTTTTGTCCAAAGAGGATAATAGC
CTAGCTTTTTAGCAACTATTCCACAACGAATCATTCCTTTCTTCCATTCTTTTGGTTCAA
CTGTCGGTACTTTTAATAAAGATGCTTTTTCATGATCTTTTTTCGACATTTCATTGATAA
ATCTTTTATTTCTTTCCGTCAGATTATCATCTCGGTCCTTTGCTCTTCTTTCGACTCTAA
AATGCCATTCAGGTACTCGTAATTTAGGGATAAATTTAAATCGATGGAAACAAACTTGTG
TTTACCTAACATCATTAATAATTGAAGTACCTAAAACAGTTTTTATGGTTTTTGATAAAA
ACATATTGAAACATTCGCTATTTCAAGTAGAAATTTAATTTTTAATTTTACTCTGCAATA
ACAGA

>g721.t20 Gene=g721 Length=147
MMTITEVYCRINRARGLELVSPEDVLNACKLLNGPMKLRQYPSGAMILQLENHNDDQVAE
EIEKLVIESESMSIEECARLKNISVLLAHERFLISENAGKICRDESVEGLRFYIIFNAKH
IHFLFLGLKCYRQISKFVNCFFINVFR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g721.t20 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 51 0
4 g721.t20 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 52 117 0
2 g721.t20 PANTHER PTHR13128 VACUOLAR PROTEIN-SORTING-ASSOCIATED PROTEIN 36 1 114 0
1 g721.t20 Pfam PF04157 EAP30/Vps36 family 1 105 0
3 g721.t20 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 15 114 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:0032509 endosome transport via multivesicular body sorting pathway BP
GO:0043130 ubiquitin binding MF
GO:0000814 ESCRT II complex CC

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