Gene loci information

Transcript annotation

  • This transcript has been annotated as Heparan-sulfate 6-O-sulfotransferase 3-B.

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 g3819 g3819.t1 TTS g3819.t1 28177255 28177255
chr_3 g3819 g3819.t1 isoform g3819.t1 28177355 28179440
chr_3 g3819 g3819.t1 exon g3819.t1.exon1 28177355 28177472
chr_3 g3819 g3819.t1 cds g3819.t1.CDS1 28177355 28177472
chr_3 g3819 g3819.t1 exon g3819.t1.exon2 28177535 28177754
chr_3 g3819 g3819.t1 cds g3819.t1.CDS2 28177535 28177754
chr_3 g3819 g3819.t1 exon g3819.t1.exon3 28177822 28177944
chr_3 g3819 g3819.t1 cds g3819.t1.CDS3 28177822 28177944
chr_3 g3819 g3819.t1 exon g3819.t1.exon4 28178003 28178059
chr_3 g3819 g3819.t1 cds g3819.t1.CDS4 28178003 28178059
chr_3 g3819 g3819.t1 exon g3819.t1.exon5 28178127 28178218
chr_3 g3819 g3819.t1 cds g3819.t1.CDS5 28178127 28178218
chr_3 g3819 g3819.t1 exon g3819.t1.exon6 28178285 28178435
chr_3 g3819 g3819.t1 cds g3819.t1.CDS6 28178285 28178435
chr_3 g3819 g3819.t1 exon g3819.t1.exon7 28178505 28178595
chr_3 g3819 g3819.t1 cds g3819.t1.CDS7 28178505 28178595
chr_3 g3819 g3819.t1 exon g3819.t1.exon8 28178661 28178711
chr_3 g3819 g3819.t1 cds g3819.t1.CDS8 28178661 28178711
chr_3 g3819 g3819.t1 exon g3819.t1.exon9 28178872 28178892
chr_3 g3819 g3819.t1 cds g3819.t1.CDS9 28178872 28178892
chr_3 g3819 g3819.t1 exon g3819.t1.exon10 28179000 28179440
chr_3 g3819 g3819.t1 cds g3819.t1.CDS10 28179000 28179440
chr_3 g3819 g3819.t1 TSS g3819.t1 28179647 28179647

Sequences

>g3819.t1 Gene=g3819 Length=1365
ATGTCAGCGATAGAAGTTAAGGCAAAGTTAAAATATGAAAAATGTGAGAATAGGCAGCAA
AGTAATGTTTCAAAGTCAGATTTGGTTTTTCTTATCGATAATCATAGTCGTAATGATGCC
ATAAAAATGGACAATTTAAAGAAGAGGCGCAAACGTTTAGTGATATTTTTAATTATCGTA
GTGCTGTCATTGTTCTCAATAGTACTTTTTGGAAGAAGTTTAAATAGTGAGGAAGTTTGT
GCATTATCGCTTTCGTTAACGAGAAAAAAATTATTTAATAACGATAATCACATCAGCAAC
AATAATATCAATAATCACAATAACAGTAGTAGCCTTAATGGTAAAAGTACCAGTAGCCAT
CTCCATCTCCTTTTAAGTTACGATGATGTCCTCAATGATGATATACAGAATAAATTTGAT
ATAAATTCAAATGATGTTATGGTCTTTCTACACATTCAGAAGACCGGTGGAACTTCGTTC
GGAAAGCATTTAGTAAGAGATTTAGATTTAAAGAGAAAATGCACATGCCAGAGAAAGAAA
AAACGATGTTACTGCTTTAGACCAAATAGAAATGAAAATTGGCTATTTAGTCGATACTCG
ACAGGTTGGAAGTGTGGCTTGCATGCCGATTGGACTGAACTCATTTCTTGTGTTGACCAA
GAGTTTGATAAAAATGAGGGTGAGACAACGAAAAGAAGATACTTTTATATTACACTCTTA
AGATCGCCTATCGCTCGATATCTGTCAGAATATAGACATGTACAACGAGGAGCAACATGG
AAAAATTCTAGACATTTTTGTCTTGGTCGTCAAGCGACGAGTGAAGAACTTCCGCCGTGT
TACACAGGAGACGACTGGATGGATGTAACTTTGGACGAGTTTGCAGATTGTGAAAGTAAT
TTGGCTGCAAACCGTCAAACTCGAATGCTCGCTGATTTAGCACTAGTTAACTGTTACAAT
AAGACTGGCATGTCATCTGAAGAAAGAGACAGAATTATGCTTGCAAGTGCAAAAAGAAAC
TTGGCGGCCATGTCATTCTTTGGTCTAACCGAGTATCAAAAAATTTCACAATACATTTTT
GAAGAAACTTTCAATCTCAGGTTTGCAATTCCTTTTGAACAGCACAACTCAACATTGTCC
ATGCAAGCATTTGAAAGCTTAACTGAAGCTCAACAAACAAAAATTAAAAAGATTAATGCA
CTCGATATAGAACTTTATGATTTTGCTAAAGAATTAATGTTTCAAAGATTTAAAAGACTC
AAAGCCAAAGATAGCGATTTTAATTTTCATTTTTCTAATTTAGGTAATATTAGAGATAAA
GGAAGCGAATTTAATTGGGACACTGTAATGGATAATGTAAATTAA

>g3819.t1 Gene=g3819 Length=454
MSAIEVKAKLKYEKCENRQQSNVSKSDLVFLIDNHSRNDAIKMDNLKKRRKRLVIFLIIV
VLSLFSIVLFGRSLNSEEVCALSLSLTRKKLFNNDNHISNNNINNHNNSSSLNGKSTSSH
LHLLLSYDDVLNDDIQNKFDINSNDVMVFLHIQKTGGTSFGKHLVRDLDLKRKCTCQRKK
KRCYCFRPNRNENWLFSRYSTGWKCGLHADWTELISCVDQEFDKNEGETTKRRYFYITLL
RSPIARYLSEYRHVQRGATWKNSRHFCLGRQATSEELPPCYTGDDWMDVTLDEFADCESN
LAANRQTRMLADLALVNCYNKTGMSSEERDRIMLASAKRNLAAMSFFGLTEYQKISQYIF
EETFNLRFAIPFEQHNSTLSMQAFESLTEAQQTKIKKINALDIELYDFAKELMFQRFKRL
KAKDSDFNFHFSNLGNIRDKGSEFNWDTVMDNVN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3819.t1 Gene3D G3DSA:3.40.50.300 - 140 439 1.2E-10
2 g3819.t1 PANTHER PTHR12812 HEPARAN SULFATE 6-O-SULFOTRANSFERASE 3 133 424 2.9E-120
3 g3819.t1 PANTHER PTHR12812:SF3 HEPARAN-SULFATE 6-O-SULFOTRANSFERASE 3 133 424 2.9E-120
1 g3819.t1 Pfam PF03567 Sulfotransferase family 138 409 1.1E-63
7 g3819.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 52 -
9 g3819.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 71 -
8 g3819.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 72 454 -
5 g3819.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 134 292 1.18E-5
4 g3819.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 53 70 -

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
GO:0016021 integral component of membrane CC

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.

Raw TPM values