Gene loci information

Transcript annotation

  • This transcript has been annotated as Beta-glucuronidase .

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 g3920 g3920.t4 TTS g3920.t4 28902789 28902789
chr_3 g3920 g3920.t4 isoform g3920.t4 28902856 28910681
chr_3 g3920 g3920.t4 exon g3920.t4.exon1 28902856 28903046
chr_3 g3920 g3920.t4 cds g3920.t4.CDS1 28902856 28903046
chr_3 g3920 g3920.t4 exon g3920.t4.exon2 28903113 28903218
chr_3 g3920 g3920.t4 cds g3920.t4.CDS2 28903113 28903218
chr_3 g3920 g3920.t4 exon g3920.t4.exon3 28903277 28903715
chr_3 g3920 g3920.t4 cds g3920.t4.CDS3 28903277 28903715
chr_3 g3920 g3920.t4 exon g3920.t4.exon4 28903790 28903882
chr_3 g3920 g3920.t4 cds g3920.t4.CDS4 28903790 28903882
chr_3 g3920 g3920.t4 exon g3920.t4.exon5 28904770 28905511
chr_3 g3920 g3920.t4 cds g3920.t4.CDS5 28904770 28905511
chr_3 g3920 g3920.t4 exon g3920.t4.exon6 28905582 28905733
chr_3 g3920 g3920.t4 cds g3920.t4.CDS6 28905582 28905733
chr_3 g3920 g3920.t4 exon g3920.t4.exon7 28905800 28905873
chr_3 g3920 g3920.t4 cds g3920.t4.CDS7 28905800 28905873
chr_3 g3920 g3920.t4 exon g3920.t4.exon8 28905930 28906117
chr_3 g3920 g3920.t4 cds g3920.t4.CDS8 28905930 28906117
chr_3 g3920 g3920.t4 exon g3920.t4.exon9 28910525 28910681
chr_3 g3920 g3920.t4 cds g3920.t4.CDS9 28910525 28910576
chr_3 g3920 g3920.t4 TSS g3920.t4 NA NA

Sequences

>g3920.t4 Gene=g3920 Length=2142
AGTTGTGGTCTGTAAGTAAAAGTGAGAACGCGCAAGCATGTTTTCTGTTTAGTTCTAACT
CGCCACGATATATTTAGTTACAATTTGTTCGAGCTATGAATAGGAATGTTAATAAAATTC
GAGCGATTAAAACGTTGTGGACTTTTTGTATCAATTGCGATCACTTTCTTTCTTATGGGA
ATTATTGGATATTTGGCTCACGTTGTATTTGGAACAATGCTATTAGCTGGAAATGAAAAA
GTTACAGCAGGCTTGCTGTATCCACGTGAATCTGAAACTCGAGAAGTCCGATCACTTGAT
GGAATGTGGAAATTCGCAAGAAGTGAAACAGACAAACCATCTCAGGGTTTGAGAGAGAAA
TGGTATTTAAAAGATTTAGAAAAATCAATCAATATTACACAAATGCCAGTGCCATCAAGC
TATAACGACATCGTCGAAGACGAAAAAGTTAGAGACCATGTCGGGACTGTTTGGTATGAA
AGAAAATTTTTTGTACCACAATCATGGAAGAGTCAACGAGTTTTTGTACGTTTTGGGAGT
GTTCATTATGAGGCATATGTATGGATAAATGGAAATTTAGCAGTGCGTCACGAATTTGGT
CATTTACCATTTGAAGCTGAAATTTCTGAGCATTTAAATTATGCCAAAGAAAATCGTATT
ACTGTATTATGTGATAATGTTTTATTACAAACAACAATTCCACAAGGAAAAGTTATAGAA
CAAGATTCAGATTCTGGCAAAGAAATTGTACAGCAATATAGTTTTGATTTTTTCAATTAT
GCTGGCATTCATCGATCAGTTCATTTATATACTGTGCCACAACTATTTATAAAAGAAGTA
ATTCTCAATCCACAAGTGACAGAAGAACGTCATGGATTAGTGAATTATAAAATTATTTTA
AGTGACAATAATGTGAATGCCAGTGACTATAAAATTAGAGTAGTTATTTTAAATAAGGAA
AATGAAAATGTTGCTGAGGCAGTTGCTGATGATGATTTTACAGGCCAAGTGCTTGTACAT
AATGCCGAATTATGGTGGCCATATTTGATGAATATTAAGCCTGGATATTTATACACGATT
GAAGTCCATTTAGTTAACGAACAGCATGATGTAGACATTGACGTGTATCGCATGAAATTT
GGAATTAGATCGCTTAAGTGGAATAATTCATCATTTTTAATCAACGATAAACCAATATAC
TTTAGAGGATTTGGTAGGCATGAGGATAGCGATATCCGCGGAAAGGGTCTTGACTTTGCT
TTGCTAACTAAAGATTTTAATTTGCTTAAATGGATTGGTGCTAATGCTTACAGAACAAGC
CATTATCCATATTCAGAAGAGTCAATGCAATTTGCTGATGAACATGGTATTATGATAATC
GATGAATGTCCATCTGTTGATACAGAAAATTATAGTCAAAAATTACTCGAAAACCACAAA
TATAGTATTGAGCAGCTTATTCATCGTGATATAAATCATCCATCCGTGGTGATGTGGTCA
ATAGCAAATGAGCCCAGAACTCAGCAAGTGAATGCTGACCAATATTTTGCAGAGGTTGCG
CGCTATACACGATTTCTGGATCCAACACGGCCAGTGACTGCAGCAATTGCCGTTAATTCT
AAGCAAGATCAAGCAGCACAGTATTTGGATATAATAAGTTTTAATAGATATAATGCATGG
TACCAAAATACAGGCAGATTAGATATGGTAACAAGTTATGTGATGAATGAGGCTAGAACT
TGGCATGAGAAACACAATAAGCCAGTGCTAATGAGTGAATATGGTAGTGACACTGTTGAA
GGACTTCACATTTTACCTGCTTACGTATGGTCGGAAGAATTCCAGAGTCAACAATTTTCA
AAGCACTTCAAAGCATTCGATCAACTGAGAAATGAGGGATTTTTCATTGGTGAATTTGTT
TGGAATTTCGCTGATTTTAAAACAGCACAAACTTATACACGTGTCGGTGGAAATAAGAAG
GGAGTTTTTACTCGTAATAGACAGCCAAAAGCAGCTGCTCATCTTTTGAGAAAGCGATAC
TATGAATTAGCATCAGAATTAGATAGTATTCATCAAAAACCTGATAATCTTTACGAATAC
ACTAGTCAAAGTCAGAACAAATTGCAAAAGAATGAACTTTAA

>g3920.t4 Gene=g3920 Length=678
MLIKFERLKRCGLFVSIAITFFLMGIIGYLAHVVFGTMLLAGNEKVTAGLLYPRESETRE
VRSLDGMWKFARSETDKPSQGLREKWYLKDLEKSINITQMPVPSSYNDIVEDEKVRDHVG
TVWYERKFFVPQSWKSQRVFVRFGSVHYEAYVWINGNLAVRHEFGHLPFEAEISEHLNYA
KENRITVLCDNVLLQTTIPQGKVIEQDSDSGKEIVQQYSFDFFNYAGIHRSVHLYTVPQL
FIKEVILNPQVTEERHGLVNYKIILSDNNVNASDYKIRVVILNKENENVAEAVADDDFTG
QVLVHNAELWWPYLMNIKPGYLYTIEVHLVNEQHDVDIDVYRMKFGIRSLKWNNSSFLIN
DKPIYFRGFGRHEDSDIRGKGLDFALLTKDFNLLKWIGANAYRTSHYPYSEESMQFADEH
GIMIIDECPSVDTENYSQKLLENHKYSIEQLIHRDINHPSVVMWSIANEPRTQQVNADQY
FAEVARYTRFLDPTRPVTAAIAVNSKQDQAAQYLDIISFNRYNAWYQNTGRLDMVTSYVM
NEARTWHEKHNKPVLMSEYGSDTVEGLHILPAYVWSEEFQSQQFSKHFKAFDQLRNEGFF
IGEFVWNFADFKTAQTYTRVGGNKKGVFTRNRQPKAAAHLLRKRYYELASELDSIHQKPD
NLYEYTSQSQNKLQKNEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g3920.t4 Gene3D G3DSA:2.60.120.260 - 50 238 7.6E-70
13 g3920.t4 Gene3D G3DSA:2.60.40.10 Immunoglobulins 240 349 1.9E-23
15 g3920.t4 Gene3D G3DSA:3.20.20.80 Glycosidases 350 656 7.1E-86
4 g3920.t4 PANTHER PTHR10066 BETA-GLUCURONIDASE 36 659 2.1E-261
9 g3920.t4 PRINTS PR00132 Glycosyl hydrolase family 2 signature 146 161 2.9E-20
5 g3920.t4 PRINTS PR00132 Glycosyl hydrolase family 2 signature 359 373 2.9E-20
7 g3920.t4 PRINTS PR00132 Glycosyl hydrolase family 2 signature 390 408 2.9E-20
6 g3920.t4 PRINTS PR00132 Glycosyl hydrolase family 2 signature 455 470 2.9E-20
8 g3920.t4 PRINTS PR00132 Glycosyl hydrolase family 2 signature 552 567 2.9E-20
1 g3920.t4 Pfam PF02837 Glycosyl hydrolases family 2, sugar binding domain 62 238 5.6E-26
2 g3920.t4 Pfam PF00703 Glycosyl hydrolases family 2 241 348 2.1E-6
3 g3920.t4 Pfam PF02836 Glycosyl hydrolases family 2, TIM barrel domain 353 648 1.4E-75
16 g3920.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
18 g3920.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
17 g3920.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 36 678 -
20 g3920.t4 ProSitePatterns PS00719 Glycosyl hydrolases family 2 signature 1. 400 425 -
10 g3920.t4 SUPERFAMILY SSF49785 Galactose-binding domain-like 49 239 1.02E-54
11 g3920.t4 SUPERFAMILY SSF49303 beta-Galactosidase/glucuronidase domain 242 349 1.04E-14
12 g3920.t4 SUPERFAMILY SSF51445 (Trans)glycosidases 351 645 2.09E-80
19 g3920.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -

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:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds MF
GO:0005975 carbohydrate metabolic process BP

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