General information for g3920.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Beta-glucuronidase .
Parent gene
- The parent gene g3920 is located on chr_3: 28904901..28910681 (- strand)
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.t1 | TTS | g3920.t1 | 28902789 | 28902789 |
| chr_3 | g3920 | g3920.t1 | isoform | g3920.t1 | 28902856 | 28906166 |
| chr_3 | g3920 | g3920.t1 | exon | g3920.t1.exon1 | 28902856 | 28903046 |
| chr_3 | g3920 | g3920.t1 | cds | g3920.t1.CDS1 | 28902856 | 28903046 |
| chr_3 | g3920 | g3920.t1 | exon | g3920.t1.exon2 | 28903113 | 28903218 |
| chr_3 | g3920 | g3920.t1 | cds | g3920.t1.CDS2 | 28903113 | 28903218 |
| chr_3 | g3920 | g3920.t1 | exon | g3920.t1.exon3 | 28903277 | 28903715 |
| chr_3 | g3920 | g3920.t1 | cds | g3920.t1.CDS3 | 28903277 | 28903715 |
| chr_3 | g3920 | g3920.t1 | exon | g3920.t1.exon4 | 28903790 | 28903882 |
| chr_3 | g3920 | g3920.t1 | cds | g3920.t1.CDS4 | 28903790 | 28903882 |
| chr_3 | g3920 | g3920.t1 | exon | g3920.t1.exon5 | 28904770 | 28905511 |
| chr_3 | g3920 | g3920.t1 | cds | g3920.t1.CDS5 | 28904770 | 28905511 |
| chr_3 | g3920 | g3920.t1 | exon | g3920.t1.exon6 | 28905582 | 28905733 |
| chr_3 | g3920 | g3920.t1 | cds | g3920.t1.CDS6 | 28905582 | 28905733 |
| chr_3 | g3920 | g3920.t1 | exon | g3920.t1.exon7 | 28905800 | 28905873 |
| chr_3 | g3920 | g3920.t1 | cds | g3920.t1.CDS7 | 28905800 | 28905873 |
| chr_3 | g3920 | g3920.t1 | exon | g3920.t1.exon8 | 28905930 | 28906166 |
| chr_3 | g3920 | g3920.t1 | cds | g3920.t1.CDS8 | 28905930 | 28906166 |
| chr_3 | g3920 | g3920.t1 | TSS | g3920.t1 | NA | NA |
Sequences
>g3920.t1 Gene=g3920 Length=2034
ATGGCACGAGTTCTTGCTGTAATTCGTAAAAAATCTTGTATGTTTACAGCGATCACTTTC
TTTCTTATGGGAATTATTGGATATTTGGCTCACGTTGTATTTGGAACAATGCTATTAGCT
GGAAATGAAAAAGTTACAGCAGGCTTGCTGTATCCACGTGAATCTGAAACTCGAGAAGTC
CGATCACTTGATGGAATGTGGAAATTCGCAAGAAGTGAAACAGACAAACCATCTCAGGGT
TTGAGAGAGAAATGGTATTTAAAAGATTTAGAAAAATCAATCAATATTACACAAATGCCA
GTGCCATCAAGCTATAACGACATCGTCGAAGACGAAAAAGTTAGAGACCATGTCGGGACT
GTTTGGTATGAAAGAAAATTTTTTGTACCACAATCATGGAAGAGTCAACGAGTTTTTGTA
CGTTTTGGGAGTGTTCATTATGAGGCATATGTATGGATAAATGGAAATTTAGCAGTGCGT
CACGAATTTGGTCATTTACCATTTGAAGCTGAAATTTCTGAGCATTTAAATTATGCCAAA
GAAAATCGTATTACTGTATTATGTGATAATGTTTTATTACAAACAACAATTCCACAAGGA
AAAGTTATAGAACAAGATTCAGATTCTGGCAAAGAAATTGTACAGCAATATAGTTTTGAT
TTTTTCAATTATGCTGGCATTCATCGATCAGTTCATTTATATACTGTGCCACAACTATTT
ATAAAAGAAGTAATTCTCAATCCACAAGTGACAGAAGAACGTCATGGATTAGTGAATTAT
AAAATTATTTTAAGTGACAATAATGTGAATGCCAGTGACTATAAAATTAGAGTAGTTATT
TTAAATAAGGAAAATGAAAATGTTGCTGAGGCAGTTGCTGATGATGATTTTACAGGCCAA
GTGCTTGTACATAATGCCGAATTATGGTGGCCATATTTGATGAATATTAAGCCTGGATAT
TTATACACGATTGAAGTCCATTTAGTTAACGAACAGCATGATGTAGACATTGACGTGTAT
CGCATGAAATTTGGAATTAGATCGCTTAAGTGGAATAATTCATCATTTTTAATCAACGAT
AAACCAATATACTTTAGAGGATTTGGTAGGCATGAGGATAGCGATATCCGCGGAAAGGGT
CTTGACTTTGCTTTGCTAACTAAAGATTTTAATTTGCTTAAATGGATTGGTGCTAATGCT
TACAGAACAAGCCATTATCCATATTCAGAAGAGTCAATGCAATTTGCTGATGAACATGGT
ATTATGATAATCGATGAATGTCCATCTGTTGATACAGAAAATTATAGTCAAAAATTACTC
GAAAACCACAAATATAGTATTGAGCAGCTTATTCATCGTGATATAAATCATCCATCCGTG
GTGATGTGGTCAATAGCAAATGAGCCCAGAACTCAGCAAGTGAATGCTGACCAATATTTT
GCAGAGGTTGCGCGCTATACACGATTTCTGGATCCAACACGGCCAGTGACTGCAGCAATT
GCCGTTAATTCTAAGCAAGATCAAGCAGCACAGTATTTGGATATAATAAGTTTTAATAGA
TATAATGCATGGTACCAAAATACAGGCAGATTAGATATGGTAACAAGTTATGTGATGAAT
GAGGCTAGAACTTGGCATGAGAAACACAATAAGCCAGTGCTAATGAGTGAATATGGTAGT
GACACTGTTGAAGGACTTCACATTTTACCTGCTTACGTATGGTCGGAAGAATTCCAGAGT
CAACAATTTTCAAAGCACTTCAAAGCATTCGATCAACTGAGAAATGAGGGATTTTTCATT
GGTGAATTTGTTTGGAATTTCGCTGATTTTAAAACAGCACAAACTTATACACGTGTCGGT
GGAAATAAGAAGGGAGTTTTTACTCGTAATAGACAGCCAAAAGCAGCTGCTCATCTTTTG
AGAAAGCGATACTATGAATTAGCATCAGAATTAGATAGTATTCATCAAAAACCTGATAAT
CTTTACGAATACACTAGTCAAAGTCAGAACAAATTGCAAAAGAATGAACTTTAA
>g3920.t1 Gene=g3920 Length=677
MARVLAVIRKKSCMFTAITFFLMGIIGYLAHVVFGTMLLAGNEKVTAGLLYPRESETREV
RSLDGMWKFARSETDKPSQGLREKWYLKDLEKSINITQMPVPSSYNDIVEDEKVRDHVGT
VWYERKFFVPQSWKSQRVFVRFGSVHYEAYVWINGNLAVRHEFGHLPFEAEISEHLNYAK
ENRITVLCDNVLLQTTIPQGKVIEQDSDSGKEIVQQYSFDFFNYAGIHRSVHLYTVPQLF
IKEVILNPQVTEERHGLVNYKIILSDNNVNASDYKIRVVILNKENENVAEAVADDDFTGQ
VLVHNAELWWPYLMNIKPGYLYTIEVHLVNEQHDVDIDVYRMKFGIRSLKWNNSSFLIND
KPIYFRGFGRHEDSDIRGKGLDFALLTKDFNLLKWIGANAYRTSHYPYSEESMQFADEHG
IMIIDECPSVDTENYSQKLLENHKYSIEQLIHRDINHPSVVMWSIANEPRTQQVNADQYF
AEVARYTRFLDPTRPVTAAIAVNSKQDQAAQYLDIISFNRYNAWYQNTGRLDMVTSYVMN
EARTWHEKHNKPVLMSEYGSDTVEGLHILPAYVWSEEFQSQQFSKHFKAFDQLRNEGFFI
GEFVWNFADFKTAQTYTRVGGNKKGVFTRNRQPKAAAHLLRKRYYELASELDSIHQKPDN
LYEYTSQSQNKLQKNEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g3920.t1 | Gene3D | G3DSA:2.60.120.260 | - | 49 | 237 | 7.6E-70 |
| 13 | g3920.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 239 | 348 | 1.9E-23 |
| 15 | g3920.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 349 | 655 | 7.0E-86 |
| 4 | g3920.t1 | PANTHER | PTHR10066 | BETA-GLUCURONIDASE | 35 | 658 | 2.1E-261 |
| 9 | g3920.t1 | PRINTS | PR00132 | Glycosyl hydrolase family 2 signature | 145 | 160 | 2.9E-20 |
| 8 | g3920.t1 | PRINTS | PR00132 | Glycosyl hydrolase family 2 signature | 358 | 372 | 2.9E-20 |
| 6 | g3920.t1 | PRINTS | PR00132 | Glycosyl hydrolase family 2 signature | 389 | 407 | 2.9E-20 |
| 5 | g3920.t1 | PRINTS | PR00132 | Glycosyl hydrolase family 2 signature | 454 | 469 | 2.9E-20 |
| 7 | g3920.t1 | PRINTS | PR00132 | Glycosyl hydrolase family 2 signature | 551 | 566 | 2.9E-20 |
| 1 | g3920.t1 | Pfam | PF02837 | Glycosyl hydrolases family 2, sugar binding domain | 61 | 237 | 5.6E-26 |
| 2 | g3920.t1 | Pfam | PF00703 | Glycosyl hydrolases family 2 | 240 | 347 | 2.1E-6 |
| 3 | g3920.t1 | Pfam | PF02836 | Glycosyl hydrolases family 2, TIM barrel domain | 352 | 647 | 1.4E-75 |
| 16 | g3920.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 18 | g3920.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
| 17 | g3920.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 35 | 677 | - |
| 20 | g3920.t1 | ProSitePatterns | PS00719 | Glycosyl hydrolases family 2 signature 1. | 399 | 424 | - |
| 10 | g3920.t1 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 48 | 238 | 1.02E-54 |
| 11 | g3920.t1 | SUPERFAMILY | SSF49303 | beta-Galactosidase/glucuronidase domain | 241 | 348 | 1.04E-14 |
| 12 | g3920.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 350 | 644 | 2.09E-80 |
| 19 | g3920.t1 | 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
- This transcript has been annotated with K01195 (beta-glucuronidase)
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.
