SoyBase
SoyBase transitions to NEW site on 10/1/2024
Integrating Genetics and Genomics to Advance Soybean Research
SoyBase
SoyBase transitions to NEW site on 10/1/2024
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A newer version of this gene model can be found here:
| Database ID | Annotation Type | Annotation Description | Annotation Source | Match Score | Evidence Code |
|---|---|---|---|---|---|
| AT1G33980 | AT | Annotation by Michelle Graham. TAIR10: Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 | SoyBase | E_val: 7.00E-111 | ISS |
| GO:0000184 | GO-bp | Annotation by Michelle Graham. GO Biological Process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | SoyBase | N/A | ISS |
| GO:0000956 | GO-bp | Annotation by Michelle Graham. GO Biological Process: nuclear-transcribed mRNA catabolic process | SoyBase | N/A | ISS |
| GO:0042742 | GO-bp | Annotation by Michelle Graham. GO Biological Process: defense response to bacterium | SoyBase | N/A | ISS |
| GO:0005634 | GO-cc | Annotation by Michelle Graham. GO Cellular Compartment: nucleus | SoyBase | N/A | ISS |
| GO:0005730 | GO-cc | Annotation by Michelle Graham. GO Cellular Compartment: nucleolus | SoyBase | N/A | ISS |
| GO:0000166 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: nucleotide binding | SoyBase | N/A | ISS |
| PTHR13112 | Panther | UPF3 REGULATOR OF NONSENSE TRANSCRIPTS-LIKE PROTEIN | JGI | ISS | |
| PF03467 | PFAM | Smg-4/UPF3 family | JGI | ISS | |
| UniRef100_I1LTB2 | UniRef | Annotation by Michelle Graham. Best UniRef hit: Uncharacterized protein n=1 Tax=Glycine max RepID=I1LTB2_SOYBN | SoyBase | E_val: 0 | ISS |
| UniRef100_Q1SL19 | UniRef | Annotation by Michelle Graham. Most informative UniRef hit: Nonsense-mediated decay UPF3 n=1 Tax=Medicago truncatula RepID=Q1SL19_MEDTR | SoyBase | E_val: 0 | ISS |
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Glyma12g28710 not represented in the dataset |
Glyma12g28710 not represented in the dataset |
| Libault et al. 2010, Plant Phys 152(2):541-552. Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection |
Severin et al. 2010, BMC Plant Biology 10:160 RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome |
| Paralog | Evidence | Comments |
|---|---|---|
| Glyma16g00390 | IGC | Paralogs in soybean determined by Steven Cannon using BLAST, DAGChainer, PAML, and selection of gene pairs from synteny blocks with median Ks values of less than 0.3. |
| Corresponding Name | Annotation Version | Evidence | Comments |
|---|---|---|---|
| Glyma.12g165900 | Wm82.a2.v1 | IGC | As supplied by JGI |
| Schmutz et al. 2010 Genome sequence of the palaeopolyploid soybean Nature 2010, 463:178-183 |
>Glyma12g28710.1 sequence type=CDS gene model=Glyma12g28710 sequence assembly version=Glyma 1.0 annotation version=1.1 JGI Gene Call confidence=high ATGAAGGGTGCGTTGGATCGGACGAAGGTGGTGCTGCGCCACTTGCCGCCTTCTATTTCTGAGGCCGCCCTTTTGTCCCAAATTGATGCGGCCTTCGCTGGCCGCTACAACTGGCTCTCTTTCCGTCCCGGCAAGATCAGCCAGAAGCATATGTCATTTTCTAGAGCCTACATTGACTTCAAGAGGCCAGAGGACGTTATATTGTTTGCCGAGTTCTTTAACGGACACGTCTTTGTGAATGTAAAGGGATCTCAGTTCAAAGTCATTGTTGAATATGCTCCTTCACAACGTGTTCCAAGACAGTGGTCTAAAAAGGATCTTCGTGATGGAACCATATATAAAGATTCTGAGTATCTGGAGTTTCTTGAACTACTTGCCAAGCCTGTTGAGAATCTTCCCAGTGCCGAGATACAATTGGAGAAGAGGGAAGCAGAACGATCTGGTGCTGCAAAAGATATTCCTATAATTACACCACTGATGGACTTTGTGCGCCAGAAAAGAGCTGCCAAGGGACCTAGGAGGCCACTGTCAAATGGAAAAGTGAGTAGAAGAGCTGGCACTTCATCAAATGGGGGCCCTAGTTCCGCCACATCAAGACGTGGTTCTGGAAAGAAGAGGGTTTCTGCTACAATGTATGTTGCAAGGGACCCAGGGAAAAGTTCTACTATCAAAGACAAATCATCTTATACTTTGGTTCCTAAGCAAGATGATCAGCATCTTCCAAATAAAGCTTCAAACATGGCTTCTTCAGATGGAAATCAAACTCTTGATGAGAATGGAGTTTCTGGAAATCATGATGCTGGGAAGAAAAAAGTACTACTTCTTAAAGGGAAGGAAAGAGAAATAATTACTGTATCTGATTTAGATAGCATGTCACAGCATCACAATGTAACATCTTCAGCTAAAACAGTTGTTGGTTCAACAGTTTTGAAACAGAGTCAGCGGCATGAAGGTAGTGGAAGGATTATCAGAAGCATACTCTCAAAAAAGGAGTTGCATCAAAGCCAGTCTTCCAGGGCCCTCTCTGAGCAGAAAATCCTGACATCCAATCTAGAGAAAGAAAAACAGCCCCCTCGCCCCTTACATGTCCAACTAATTTTGAAGGGCTCTAATGGGACACCAGAGAATAAGATTGGTGTGCATGATTCACATGTTTCTAGTGAGAGGCAAGAGAGACATGTTAGACATAAAGATAGACCTGATCGTGGTGTCTGGACAAGTCGTTTCAATGGAGCTGACGTGTCTTTCTCATCTCCTGCTTCCTCACAAGTAGATCCTTTGGAAGGAAGTCAAGCAGATTTGAAACATGACATGCCAAATGCAAGAAGTGTGGAGGTAAAATCTTTTGGAAGTGTCCGTACCAGTCATTCATCAGAAAATGGTTTCAATAAGCATTTTGGTCGTCGTGGACCATCATATGGGGTAAAGGATGTTGATGGCTATTCAGTTTCAAGTGAAGGGAAGCATCCTAGAAGATCTAGTACATCTGCTTATGGTTCCAACGAGAAACAAGTTTGGGTTCAAAAAGCAAGTTCTGGTAGCTAG
>Glyma12g28710.1 sequence type=predicted peptide gene model=Glyma12g28710 sequence assembly version=Glyma 1.0 annotation version=1.1 JGI Gene Call confidence=high MKGALDRTKVVLRHLPPSISEAALLSQIDAAFAGRYNWLSFRPGKISQKHMSFSRAYIDFKRPEDVILFAEFFNGHVFVNVKGSQFKVIVEYAPSQRVPRQWSKKDLRDGTIYKDSEYLEFLELLAKPVENLPSAEIQLEKREAERSGAAKDIPIITPLMDFVRQKRAAKGPRRPLSNGKVSRRAGTSSNGGPSSATSRRGSGKKRVSATMYVARDPGKSSTIKDKSSYTLVPKQDDQHLPNKASNMASSDGNQTLDENGVSGNHDAGKKKVLLLKGKEREIITVSDLDSMSQHHNVTSSAKTVVGSTVLKQSQRHEGSGRIIRSILSKKELHQSQSSRALSEQKILTSNLEKEKQPPRPLHVQLILKGSNGTPENKIGVHDSHVSSERQERHVRHKDRPDRGVWTSRFNGADVSFSSPASSQVDPLEGSQADLKHDMPNARSVEVKSFGSVRTSHSSENGFNKHFGRRGPSYGVKDVDGYSVSSEGKHPRRSSTSAYGSNEKQVWVQKASSGS*
| Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA | ||
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