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.t6 TTS g3819.t6 28177255 28177255
chr_3 g3819 g3819.t6 isoform g3819.t6 28177355 28179440
chr_3 g3819 g3819.t6 exon g3819.t6.exon1 28177355 28177445
chr_3 g3819 g3819.t6 cds g3819.t6.CDS1 28177355 28177445
chr_3 g3819 g3819.t6 exon g3819.t6.exon2 28177535 28177754
chr_3 g3819 g3819.t6 cds g3819.t6.CDS2 28177535 28177754
chr_3 g3819 g3819.t6 exon g3819.t6.exon3 28177822 28177944
chr_3 g3819 g3819.t6 cds g3819.t6.CDS3 28177822 28177944
chr_3 g3819 g3819.t6 exon g3819.t6.exon4 28178003 28178059
chr_3 g3819 g3819.t6 cds g3819.t6.CDS4 28178003 28178059
chr_3 g3819 g3819.t6 exon g3819.t6.exon5 28178127 28178218
chr_3 g3819 g3819.t6 cds g3819.t6.CDS5 28178127 28178218
chr_3 g3819 g3819.t6 exon g3819.t6.exon6 28178285 28178435
chr_3 g3819 g3819.t6 cds g3819.t6.CDS6 28178285 28178435
chr_3 g3819 g3819.t6 exon g3819.t6.exon7 28178505 28178595
chr_3 g3819 g3819.t6 cds g3819.t6.CDS7 28178505 28178595
chr_3 g3819 g3819.t6 exon g3819.t6.exon8 28178661 28178711
chr_3 g3819 g3819.t6 cds g3819.t6.CDS8 28178661 28178711
chr_3 g3819 g3819.t6 exon g3819.t6.exon9 28178872 28178892
chr_3 g3819 g3819.t6 cds g3819.t6.CDS9 28178872 28178892
chr_3 g3819 g3819.t6 exon g3819.t6.exon10 28179000 28179440
chr_3 g3819 g3819.t6 cds g3819.t6.CDS10 28179000 28179440
chr_3 g3819 g3819.t6 TSS g3819.t6 28179647 28179647

Sequences

>g3819.t6 Gene=g3819 Length=1338
ATGTCAGCGATAGAAGTTAAGGCAAAGTTAAAATATGAAAAATGTGAGAATAGGCAGCAA
AGTAATGTTTCAAAGTCAGATTTGGTTTTTCTTATCGATAATCATAGTCGTAATGATGCC
ATAAAAATGGACAATTTAAAGAAGAGGCGCAAACGTTTAGTGATATTTTTAATTATCGTA
GTGCTGTCATTGTTCTCAATAGTACTTTTTGGAAGAAGTTTAAATAGTGAGGAAGTTTGT
GCATTATCGCTTTCGTTAACGAGAAAAAAATTATTTAATAACGATAATCACATCAGCAAC
AATAATATCAATAATCACAATAACAGTAGTAGCCTTAATGGTAAAAGTACCAGTAGCCAT
CTCCATCTCCTTTTAAGTTACGATGATGTCCTCAATGATGATATACAGAATAAATTTGAT
ATAAATTCAAATGATGTTATGGTCTTTCTACACATTCAGAAGACCGGTGGAACTTCGTTC
GGAAAGCATTTAGTAAGAGATTTAGATTTAAAGAGAAAATGCACATGCCAGAGAAAGAAA
AAACGATGTTACTGCTTTAGACCAAATAGAAATGAAAATTGGCTATTTAGTCGATACTCG
ACAGGTTGGAAGTGTGGCTTGCATGCCGATTGGACTGAACTCATTTCTTGTGTTGACCAA
GAGTTTGATAAAAATGAGGGTGAGACAACGAAAAGAAGATACTTTTATATTACACTCTTA
AGATCGCCTATCGCTCGATATCTGTCAGAATATAGACATGTACAACGAGGAGCAACATGG
AAAAATTCTAGACATTTTTGTCTTGGTCGTCAAGCGACGAGTGAAGAACTTCCGCCGTGT
TACACAGGAGACGACTGGATGGATGTAACTTTGGACGAGTTTGCAGATTGTGAAAGTAAT
TTGGCTGCAAACCGTCAAACTCGAATGCTCGCTGATTTAGCACTAGTTAACTGTTACAAT
AAGACTGGCATGTCATCTGAAGAAAGAGACAGAATTATGCTTGCAAGTGCAAAAAGAAAC
TTGGCGGCCATGTCATTCTTTGGTCTAACCGAGTATCAAAAAATTTCACAATACATTTTT
GAAGAAACTTTCAATCTCAGGTTTGCAATTCCTTTTGAACAGCACAACTCAACATTGTCC
ATGCAAGCATTTGAAAGCTTAACTGAAGCTCAACAAACAAAAATTAAAAAGATTAATGCA
CTCGATATAGAACTTTATGATTTTGCTAAAGAATTAATGTTTCAAAGCGATTTTAATTTT
CATTTTTCTAATTTAGGTAATATTAGAGATAAAGGAAGCGAATTTAATTGGGACACTGTA
ATGGATAATGTAAATTAA

>g3819.t6 Gene=g3819 Length=445
MSAIEVKAKLKYEKCENRQQSNVSKSDLVFLIDNHSRNDAIKMDNLKKRRKRLVIFLIIV
VLSLFSIVLFGRSLNSEEVCALSLSLTRKKLFNNDNHISNNNINNHNNSSSLNGKSTSSH
LHLLLSYDDVLNDDIQNKFDINSNDVMVFLHIQKTGGTSFGKHLVRDLDLKRKCTCQRKK
KRCYCFRPNRNENWLFSRYSTGWKCGLHADWTELISCVDQEFDKNEGETTKRRYFYITLL
RSPIARYLSEYRHVQRGATWKNSRHFCLGRQATSEELPPCYTGDDWMDVTLDEFADCESN
LAANRQTRMLADLALVNCYNKTGMSSEERDRIMLASAKRNLAAMSFFGLTEYQKISQYIF
EETFNLRFAIPFEQHNSTLSMQAFESLTEAQQTKIKKINALDIELYDFAKELMFQSDFNF
HFSNLGNIRDKGSEFNWDTVMDNVN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3819.t6 Gene3D G3DSA:3.40.50.300 - 140 444 2.3E-10
2 g3819.t6 PANTHER PTHR12812 HEPARAN SULFATE 6-O-SULFOTRANSFERASE 3 133 419 3.0E-118
3 g3819.t6 PANTHER PTHR12812:SF3 HEPARAN-SULFATE 6-O-SULFOTRANSFERASE 3 133 419 3.0E-118
1 g3819.t6 Pfam PF03567 Sulfotransferase family 138 409 1.0E-63
7 g3819.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 52 -
9 g3819.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 71 -
8 g3819.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 72 445 -
5 g3819.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 134 292 1.12E-5
4 g3819.t6 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