Gene loci information

Transcript annotation

  • This transcript has been annotated as Chondroitin sulfate glucuronyltransferase.

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 g13171 g13171.t1 isoform g13171.t1 28318949 28321400
chr_1 g13171 g13171.t1 exon g13171.t1.exon1 28318949 28319274
chr_1 g13171 g13171.t1 cds g13171.t1.CDS1 28318949 28319274
chr_1 g13171 g13171.t1 exon g13171.t1.exon2 28319339 28321400
chr_1 g13171 g13171.t1 cds g13171.t1.CDS2 28319339 28321400
chr_1 g13171 g13171.t1 TSS g13171.t1 28321517 28321517
chr_1 g13171 g13171.t1 TTS g13171.t1 NA NA

Sequences

>g13171.t1 Gene=g13171 Length=2388
ATGTATCTTCCTAAAGTGTTTAGATTTAGGAGTTCACAACTCAGTGCTAATCAATATTTT
ATTGTATGTCTGATCGGAGGATTTTTATTAAGTTTTTATTGGCCTACATCAAGCTATCGT
GATGAAAATTGCGAACAGAAATTAAGAGAACTCGCTTCAATTAATGGCAATTCACAAAGT
CATTTACTTAATGAAGATTTCGAACCGCAGCTTAATTTAGCACAAAAACCTATGTCAGCA
AAAAAGTCAGTCAAATCGATCGTTCGTCCAAGATATTTCAGTTCAGAATTAAATGTAAAA
CAAGATCGATTATTTGTTGGTGTACTAACAGTACAAGAGAATATTGAAAGTTTGGCAACT
GCCTTCAATAAAACAACTGCACATCTAGTTAATAAGATTAAATTTTTCATTCATGCCGAT
AATATTAAGACAAATTTCAAGCTTAAAAATATTGTCGGATTTACAGATACAAGAGAGAAT
TATCGTGCATTTCATGTTTTAAAGTATATTGGAGACAATTATTTAGAGGATTATGATTTC
TTCTATATAATTGAAGATGGTGCTTATTTGAATGCAAGATCACTTATGGAGAAATTAAAT
CATATAAGCATGAGTTTTGATGTTTACTTGGGTACAAAAATTGAAGATCGTGAAGAAGGA
TTTTGTGATTTAAAAGCTGGAATTCTTTTGAGTAGCAGCGTTGTGAAAAAAATTAAATTG
AAACTTGATGCATGTGTTAGAACAGCTGATGGAACTCATCATAGTGTTAACGTTGGTAGA
TGCGTACAACTTGCTACAGACATAAAAGAGTGTCAAGAATTTTTTCAAGCTATCTCGTTG
CCAACTTATGTCCTCTCAAATCAAAAGATTTATCGAGATCTTCATTTTTTAAAAGAGGAT
ACAAATTTTAATCAAGCATCTATCATATATCCACTCACTTCAGCTGATGATCTTTACATT
CTTCATGCATATTTTTCAAAGCTTCATCTTGATGCAGTAAAGAATAAAATCTCAAAATTA
GAGGAAGAAGCTGCCCACATTGGAAATGGCACGATCTCAAATAACATTTTAGAAATTAAT
TGGCCTCTAGGAGTCAATCAAGCAATGAAACCTCAACACCGTCATGATATTATTTTATGG
ACAAATTTAAATTTAACACATAGTTTTATGAATAGTGATGGAAGCAATGTAAAAGCATTG
AGTAAAATTGATAGAATGGATATTCAAAAGATTCTTGATGGAATTCTTGCTGAAGTAAGG
AAAAAGTATCCAGAATTAAATTTTATTGAAATGCAAACTGCCTATAAAAGATTCGATCCA
GTACGAGGTATGGAATATAAAATTCATCTTGTATTTCATGATGCTGATAGAAATGAAGTT
TTAAAGAGTTATGAAGTTGTGAAACCAATTTCATTGATACAAATAATACCTAGTCCCTAT
GTAACTGAATCGACACGAATTTCAATGATTGTGCCTTCATTTACACATCGCATTGAGGAA
ACCATTAGTTTCATTGAACGATACGAGGAAATTTGTATGCAGACCAAAGACTCGACTACA
CTCATGCTCGTACTACTCTATAATTCAAATGACTCTAACAAAGGCGAATCAGACGTTTTT
TATCGTTTGAAAAATGTAGCAATTACAACGTCTAAAAGAATTAAGAATGATGATTCTAGA
ATTGCATGGGTTTCAATAAGGCTTCCGCAAGAGTTTGATTATTCATATGAGGACAGTGAT
GAGCTTCTTAGTTCACTTTATGCAAATCAAGAAATTTTATCTCTTGCTGTCACTGATCTT
GCTCTCCGAAAAATCGGTCTTGAAAGTCTAGTATTGGCCTTTTCAAATGTTGTCAATTTC
AAAAATGACTTTCTAAATCGTGTCAGAATGAACACAATTCAAGGATTTCAAATTTTCTCA
CCAATCGGTTTTATGCAATATCCTTGCAAGCAAACACAAATGTGTAATCACTGTGAAAAT
TGTGATGTTTCACAGAGCACTGGATATTTTGATAACAACAATCATGACATCATTTCATTC
TATAGCAGAGATTATGTCGATGCTAGGAAGAAACTTGAACAATATGTACCGATTGTGCGT
AAAGATGCTGACATCATCAATTTACAGACACGTCAATATAAAGATGTAACTAGAGTCATT
GATATATTTGTGCGTGCAAAAACGCAAGTACATATTTTGAGAGCGGTTGAACCTACTCTC
AGATTTGGAATCAATTTGAACAATTTTCTTGAAAAATTTCAAGGAAAGGTGTTGCCTAAA
TGCCAATATCTCAATACTACTTTAGAACACAAATGCATTAATTTGATATCTCGAAAGCAG
CTCGGCGAAGCTATTGTCGCCTATAAAAGTTCTATAAATGAATCATAA

>g13171.t1 Gene=g13171 Length=795
MYLPKVFRFRSSQLSANQYFIVCLIGGFLLSFYWPTSSYRDENCEQKLRELASINGNSQS
HLLNEDFEPQLNLAQKPMSAKKSVKSIVRPRYFSSELNVKQDRLFVGVLTVQENIESLAT
AFNKTTAHLVNKIKFFIHADNIKTNFKLKNIVGFTDTRENYRAFHVLKYIGDNYLEDYDF
FYIIEDGAYLNARSLMEKLNHISMSFDVYLGTKIEDREEGFCDLKAGILLSSSVVKKIKL
KLDACVRTADGTHHSVNVGRCVQLATDIKECQEFFQAISLPTYVLSNQKIYRDLHFLKED
TNFNQASIIYPLTSADDLYILHAYFSKLHLDAVKNKISKLEEEAAHIGNGTISNNILEIN
WPLGVNQAMKPQHRHDIILWTNLNLTHSFMNSDGSNVKALSKIDRMDIQKILDGILAEVR
KKYPELNFIEMQTAYKRFDPVRGMEYKIHLVFHDADRNEVLKSYEVVKPISLIQIIPSPY
VTESTRISMIVPSFTHRIEETISFIERYEEICMQTKDSTTLMLVLLYNSNDSNKGESDVF
YRLKNVAITTSKRIKNDDSRIAWVSIRLPQEFDYSYEDSDELLSSLYANQEILSLAVTDL
ALRKIGLESLVLAFSNVVNFKNDFLNRVRMNTIQGFQIFSPIGFMQYPCKQTQMCNHCEN
CDVSQSTGYFDNNNHDIISFYSRDYVDARKKLEQYVPIVRKDADIINLQTRQYKDVTRVI
DIFVRAKTQVHILRAVEPTLRFGINLNNFLEKFQGKVLPKCQYLNTTLEHKCINLISRKQ
LGEAIVAYKSSINES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13171.t1 PANTHER PTHR12369:SF13 HEXOSYLTRANSFERASE 13 790 5.9E-193
3 g13171.t1 PANTHER PTHR12369 CHONDROITIN SYNTHASE 13 790 5.9E-193
1 g13171.t1 Pfam PF05679 Chondroitin N-acetylgalactosaminyltransferase 242 752 7.8E-114
4 g13171.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 15 -
6 g13171.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 16 34 -
5 g13171.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 795 -

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:0032580 Golgi cisterna membrane CC
GO:0008376 acetylgalactosaminyltransferase 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