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.t5 isoform g3920.t5 28904901 28910366
chr_3 g3920 g3920.t5 exon g3920.t5.exon1 28904901 28905511
chr_3 g3920 g3920.t5 cds g3920.t5.CDS1 28904901 28905511
chr_3 g3920 g3920.t5 exon g3920.t5.exon2 28905582 28905733
chr_3 g3920 g3920.t5 cds g3920.t5.CDS2 28905582 28905733
chr_3 g3920 g3920.t5 exon g3920.t5.exon3 28905800 28905873
chr_3 g3920 g3920.t5 cds g3920.t5.CDS3 28905800 28905873
chr_3 g3920 g3920.t5 exon g3920.t5.exon4 28905930 28906117
chr_3 g3920 g3920.t5 cds g3920.t5.CDS4 28905930 28906117
chr_3 g3920 g3920.t5 exon g3920.t5.exon5 28910202 28910366
chr_3 g3920 g3920.t5 cds g3920.t5.CDS5 28910202 28910274
chr_3 g3920 g3920.t5 TSS g3920.t5 28910399 28910399
chr_3 g3920 g3920.t5 TTS g3920.t5 NA NA

Sequences

>g3920.t5 Gene=g3920 Length=1190
GTTCTAGTGTGGAAAATTTTGTAATTTCTTGAATAATTTCTTAGTGTTAAGTAAAAGAAT
AATTAGTGAATACAATTAAGAATAGTGTTTATATGCCTCTTTTATATAAGAACGATACAC
GATACTATAATCATAGATTTTCATGGCTATTTCAAGTGATTGACTCGATCACTTTCTTTC
TTATGGGAATTATTGGATATTTGGCTCACGTTGTATTTGGAACAATGCTATTAGCTGGAA
ATGAAAAAGTTACAGCAGGCTTGCTGTATCCACGTGAATCTGAAACTCGAGAAGTCCGAT
CACTTGATGGAATGTGGAAATTCGCAAGAAGTGAAACAGACAAACCATCTCAGGGTTTGA
GAGAGAAATGGTATTTAAAAGATTTAGAAAAATCAATCAATATTACACAAATGCCAGTGC
CATCAAGCTATAACGACATCGTCGAAGACGAAAAAGTTAGAGACCATGTCGGGACTGTTT
GGTATGAAAGAAAATTTTTTGTACCACAATCATGGAAGAGTCAACGAGTTTTTGTACGTT
TTGGGAGTGTTCATTATGAGGCATATGTATGGATAAATGGAAATTTAGCAGTGCGTCACG
AATTTGGTCATTTACCATTTGAAGCTGAAATTTCTGAGCATTTAAATTATGCCAAAGAAA
ATCGTATTACTGTATTATGTGATAATGTTTTATTACAAACAACAATTCCACAAGGAAAAG
TTATAGAACAAGATTCAGATTCTGGCAAAGAAATTGTACAGCAATATAGTTTTGATTTTT
TCAATTATGCTGGCATTCATCGATCAGTTCATTTATATACTGTGCCACAACTATTTATAA
AAGAAGTAATTCTCAATCCACAAGTGACAGAAGAACGTCATGGATTAGTGAATTATAAAA
TTATTTTAAGTGACAATAATGTGAATGCCAGTGACTATAAAATTAGAGTAGTTATTTTAA
ATAAGGAAAATGAAAATGTTGCTGAGGCAGTTGCTGATGATGATTTTACAGGCCAAGTGC
TTGTACATAATGCCGAATTATGGTGGCCATATTTGATGAATATTAAGCCTGGATATTTAT
ACACGATTGAAGTCCATTTAGTTAACGAACAGCATGATGTAGACATTGACGTGTATCGCA
TGAAATTTGGAATTAGATCGCTTAAGTGGAATAATTCATCATTTTTAATC

>g3920.t5 Gene=g3920 Length=366
MPLLYKNDTRYYNHRFSWLFQVIDSITFFLMGIIGYLAHVVFGTMLLAGNEKVTAGLLYP
RESETREVRSLDGMWKFARSETDKPSQGLREKWYLKDLEKSINITQMPVPSSYNDIVEDE
KVRDHVGTVWYERKFFVPQSWKSQRVFVRFGSVHYEAYVWINGNLAVRHEFGHLPFEAEI
SEHLNYAKENRITVLCDNVLLQTTIPQGKVIEQDSDSGKEIVQQYSFDFFNYAGIHRSVH
LYTVPQLFIKEVILNPQVTEERHGLVNYKIILSDNNVNASDYKIRVVILNKENENVAEAV
ADDDFTGQVLVHNAELWWPYLMNIKPGYLYTIEVHLVNEQHDVDIDVYRMKFGIRSLKWN
NSSFLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3920.t5 Gene3D G3DSA:2.60.120.260 - 57 245 2.0E-70
7 g3920.t5 Gene3D G3DSA:2.60.40.10 Immunoglobulins 247 356 6.7E-24
3 g3920.t5 PANTHER PTHR10066 BETA-GLUCURONIDASE 42 366 7.6E-108
1 g3920.t5 Pfam PF02837 Glycosyl hydrolases family 2, sugar binding domain 69 245 1.5E-26
2 g3920.t5 Pfam PF00703 Glycosyl hydrolases family 2 248 355 7.3E-7
10 g3920.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
11 g3920.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
9 g3920.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 43 366 -
5 g3920.t5 SUPERFAMILY SSF49785 Galactose-binding domain-like 56 246 2.19E-55
6 g3920.t5 SUPERFAMILY SSF49303 beta-Galactosidase/glucuronidase domain 249 356 3.74E-15
4 g3920.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 16 38 -

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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