Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Heparan sulfate glucosamine 3-O-sulfotransferase 5.

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 g3728 g3728.t2 TSS g3728.t2 27680770 27680770
chr_3 g3728 g3728.t2 isoform g3728.t2 27680901 27681794
chr_3 g3728 g3728.t2 exon g3728.t2.exon1 27680901 27681040
chr_3 g3728 g3728.t2 exon g3728.t2.exon2 27681109 27681284
chr_3 g3728 g3728.t2 cds g3728.t2.CDS1 27681138 27681284
chr_3 g3728 g3728.t2 exon g3728.t2.exon3 27681389 27681508
chr_3 g3728 g3728.t2 cds g3728.t2.CDS2 27681389 27681508
chr_3 g3728 g3728.t2 exon g3728.t2.exon4 27681579 27681794
chr_3 g3728 g3728.t2 cds g3728.t2.CDS3 27681579 27681794
chr_3 g3728 g3728.t2 TTS g3728.t2 NA NA

Sequences

>g3728.t2 Gene=g3728 Length=652
CTAATTATTTTAATTCGTTATAGTGTAGTAGAATAAAGATGTTTATTGTTTCAAATGCAT
TAAGGATAAGACAAGGATTGTATCGTTTCATGAAAAAAGACGAGCGTTTAGAATAATTTT
TTCAGCAGTCATAAAAAAAGAAAAATTAAAAATCAAACAATGAGGCGATATGAATAGCGA
TCCAGTTAATAAAGAAATAGTTATTGGCTTAGTCTCGAAGAGAAAATTGACGTTTCTGTT
TATTTTAATCATGTTAATATCGTTATTCTTCACATTCCATGTATTGTTGTACGATTCGAC
TATTTACTCCATTCAGGCAGCAACAATAATTTCAAGTAATAAGATTATACCAACGATAGC
ACCGCGTTTTAAGAAACAAATGAAATTCTCTCCATATCACATACATTTTCCAAAAACTAG
TAGAAAACTACCACAATGCTTAATTATTGGTGTAAGAAAATGTGGTACGCGTGCATTACT
GGAAATGTTGAATCTTCATCCAAGAATTCAAAAAGCGGCAGGAGAAGTTCATTTCTTCGA
TCGTGATGAGAATTATGAGCGTGGTTTAGAATGGTATCGTAAGAAAATGCCTCATAGTTT
TAGAGGACAAATTACGATTGAAAAAAGTCCAAGTTACTTTGTTACTCCTGAA

>g3728.t2 Gene=g3728 Length=161
MNSDPVNKEIVIGLVSKRKLTFLFILIMLISLFFTFHVLLYDSTIYSIQAATIISSNKII
PTIAPRFKKQMKFSPYHIHFPKTSRKLPQCLIIGVRKCGTRALLEMLNLHPRIQKAAGEV
HFFDRDENYERGLEWYRKKMPHSFRGQITIEKSPSYFVTPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3728.t2 Gene3D G3DSA:3.40.50.300 - 76 161 1.1E-31
2 g3728.t2 PANTHER PTHR10605:SF56 GH20068P 19 160 7.3E-36
3 g3728.t2 PANTHER PTHR10605 HEPARAN SULFATE SULFOTRANSFERASE 19 160 7.3E-36
1 g3728.t2 Pfam PF00685 Sulfotransferase domain 88 150 2.8E-10
8 g3728.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
10 g3728.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 40 -
9 g3728.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 41 45 -
11 g3728.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 46 64 -
7 g3728.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 65 161 -
5 g3728.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 69 160 1.51E-24
4 g3728.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 41 -

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:0008146 sulfotransferase 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