Gene loci information

Transcript annotation

  • This transcript has been annotated as Chondroitin sulfate synthase 1.

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_1 g11384 g11384.t4 TSS g11384.t4 15884879 15884879
chr_1 g11384 g11384.t4 isoform g11384.t4 15885206 15887009
chr_1 g11384 g11384.t4 exon g11384.t4.exon1 15885206 15885347
chr_1 g11384 g11384.t4 cds g11384.t4.CDS1 15885206 15885347
chr_1 g11384 g11384.t4 exon g11384.t4.exon2 15886028 15886216
chr_1 g11384 g11384.t4 cds g11384.t4.CDS2 15886028 15886216
chr_1 g11384 g11384.t4 exon g11384.t4.exon3 15886453 15886653
chr_1 g11384 g11384.t4 cds g11384.t4.CDS3 15886453 15886653
chr_1 g11384 g11384.t4 exon g11384.t4.exon4 15886726 15886839
chr_1 g11384 g11384.t4 cds g11384.t4.CDS4 15886726 15886839
chr_1 g11384 g11384.t4 exon g11384.t4.exon5 15886904 15887009
chr_1 g11384 g11384.t4 cds g11384.t4.CDS5 15886904 15887007
chr_1 g11384 g11384.t4 TTS g11384.t4 NA NA

Sequences

>g11384.t4 Gene=g11384 Length=752
ATGACACAACACTTAAAACTTTTTTATGGTCTTTTGGGAGCTGTGATAGGATTATGTATT
GGGACTTTTCTCAAAAGTTTCAATACTATGGAGACAATTACACAGTGCGACCTGTTGTCT
GCCGCAAGTGTTCAATTGAAATCACCATTACAATTAATTAATTTAACGGATGAAGAGACC
CCAGTAAACAGTCAACGAACATTGGTTTTTGTCGGCGTAATGACATCCAAAGACTTCTTA
GAATCGCGTGCAAAGTCTGTGTATAATACATGGGGTAAATCAGTTCCTGGAAGGATTGCT
TTCTTTAGTTCTGAAGGCTCAGCTATGGATGATCTTCCAGTTATTGCGCTTAATGGTGTT
GACGATCGTTATCCGCCACAACGTAAATCATTTACGATGCTACACTACATGTATGAACAT
TATATTGACAAATTCGAATGGTTTCTTCGTGCTGATGATGATGTTTTTATTAAGACGGAT
AAACTCGAAAAGTTTTTAAGACGTATCGACTCAACAAAGGCACAATTTATTGGGCAAGCA
GGGCGTGGAAATAATGAAGAATTTGGTCTTCTTTCTCTTGAGTATGACGAAAATTTTTGT
ATGGGAGGACCAGGCATAATTTTAAGTCGTCAAACTCTTAAACAAGTTGCTCCACACATT
CCTACTTGTCTAAAAAATCTCTATAGCACACATGAAGATGTTGAAGTAGGAAGATGCGTT
CAAAAATTTGCTGGAACTGCATGCACTTGGAA

>g11384.t4 Gene=g11384 Length=250
MTQHLKLFYGLLGAVIGLCIGTFLKSFNTMETITQCDLLSAASVQLKSPLQLINLTDEET
PVNSQRTLVFVGVMTSKDFLESRAKSVYNTWGKSVPGRIAFFSSEGSAMDDLPVIALNGV
DDRYPPQRKSFTMLHYMYEHYIDKFEWFLRADDDVFIKTDKLEKFLRRIDSTKAQFIGQA
GRGNNEEFGLLSLEYDENFCMGGPGIILSRQTLKQVAPHIPTCLKNLYSTHEDVEVGRCV
QKFAGTACTW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g11384.t4 Gene3D G3DSA:3.90.550.50 - 56 249 1.6E-21
2 g11384.t4 PANTHER PTHR12369 CHONDROITIN SYNTHASE 3 250 3.8E-106
3 g11384.t4 PANTHER PTHR12369:SF11 HEXOSYLTRANSFERASE 3 250 3.8E-106
1 g11384.t4 Pfam PF02434 Fringe-like 68 243 7.8E-14
6 g11384.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 6 -
8 g11384.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 7 27 -
7 g11384.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 28 250 -
4 g11384.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 24 -

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:0016020 membrane CC
GO:0016757 glycosyltransferase activity MF

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