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A newer version of this gene model can be found here: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 |
|---|---|---|---|---|---|
| AT1G03190 | AT | Annotation by Michelle Graham. TAIR10: RAD3-like DNA-binding helicase protein | chr1:775822-779863 FORWARD LENGTH=758 | SoyBase | E_val: 0 | ISS |
| GO:0000394 | GO-bp | Annotation by Michelle Graham. GO Biological Process: RNA splicing, via endonucleolytic cleavage and ligation | SoyBase | N/A | ISS |
| GO:0000724 | GO-bp | Annotation by Michelle Graham. GO Biological Process: double-strand break repair via homologous recombination | SoyBase | N/A | ISS |
| GO:0006139 | GO-bp | Annotation by Michelle Graham. GO Biological Process: nucleobase-containing compound metabolic process | SoyBase | N/A | ISS |
| GO:0006281 | GO-bp | Annotation by Michelle Graham. GO Biological Process: DNA repair | SoyBase | N/A | ISS |
| GO:0006289 | GO-bp | Annotation by Michelle Graham. GO Biological Process: nucleotide-excision repair | SoyBase | N/A | ISS |
| GO:0006355 | GO-bp | Annotation by Michelle Graham. GO Biological Process: regulation of transcription, DNA-dependent | SoyBase | N/A | ISS |
| GO:0006366 | GO-bp | Annotation by Michelle Graham. GO Biological Process: transcription from RNA polymerase II promoter | SoyBase | N/A | ISS |
| GO:0006457 | GO-bp | Annotation by Michelle Graham. GO Biological Process: protein folding | SoyBase | N/A | ISS |
| GO:0009408 | GO-bp | Annotation by Michelle Graham. GO Biological Process: response to heat | SoyBase | N/A | ISS |
| GO:0009411 | GO-bp | Annotation by Michelle Graham. GO Biological Process: response to UV | SoyBase | N/A | ISS |
| GO:0009644 | GO-bp | Annotation by Michelle Graham. GO Biological Process: response to high light intensity | SoyBase | N/A | ISS |
| GO:0010212 | GO-bp | Annotation by Michelle Graham. GO Biological Process: response to ionizing radiation | SoyBase | N/A | ISS |
| GO:0010286 | GO-bp | Annotation by Michelle Graham. GO Biological Process: heat acclimation | SoyBase | N/A | ISS |
| GO:0042542 | GO-bp | Annotation by Michelle Graham. GO Biological Process: response to hydrogen peroxide | SoyBase | N/A | ISS |
| GO:0043687 | GO-bp | Annotation by Michelle Graham. GO Biological Process: post-translational protein modification | SoyBase | N/A | ISS |
| GO:0045893 | GO-bp | Annotation by Michelle Graham. GO Biological Process: positive regulation of transcription, DNA-dependent | SoyBase | N/A | ISS |
| GO:0005634 | GO-cc | Annotation by Michelle Graham. GO Cellular Compartment: nucleus | SoyBase | N/A | ISS |
| GO:0003676 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: nucleic acid binding | SoyBase | N/A | ISS |
| GO:0003677 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: DNA binding | SoyBase | N/A | ISS |
| GO:0004003 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: ATP-dependent DNA helicase activity | SoyBase | N/A | ISS |
| GO:0005515 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: protein binding | SoyBase | N/A | ISS |
| GO:0005524 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: ATP binding | SoyBase | N/A | ISS |
| GO:0008026 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: ATP-dependent helicase activity | SoyBase | N/A | ISS |
| GO:0016817 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: hydrolase activity, acting on acid anhydrides | SoyBase | N/A | ISS |
| GO:0016818 | GO-mf | Annotation by Michelle Graham. GO Molecular Function: hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides | SoyBase | N/A | ISS |
| KOG1131 | KOG | RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 | JGI | ISS | |
| PTHR11472 | Panther | DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER | JGI | ISS | |
| PTHR11472:SF1 | Panther | gb def: atp-dependent helicase, ding family fusobacterium nucleatum subsp. nucleatum at | JGI | ISS | |
| PF06733 | PFAM | DEAD 2 | JGI | ISS | |
| PF06777 | PFAM | Protein of unknown function (DUF1227) | JGI | ISS | |
| UniRef100_B9S438 | UniRef | Annotation by Michelle Graham. Most informative UniRef hit: DNA repair helicase rad3/xp-d, putative n=1 Tax=Ricinus communis RepID=B9S438_RICCO | SoyBase | E_val: 0 | ISS |
| UniRef100_I1MP75 | UniRef | Annotation by Michelle Graham. Best UniRef hit: Uncharacterized protein n=1 Tax=Glycine max RepID=I1MP75_SOYBN | SoyBase | E_val: 0 | ISS |
|
Glyma16g28290 not represented in the dataset |
Glyma16g28290 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 |
|---|---|---|
| Glyma02g09080 | 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.16g167800 | Wm82.a2.v1 | IGC | As supplied by JGI |
| Schmutz et al. 2010 Genome sequence of the palaeopolyploid soybean Nature 2010, 463:178-183 |
>Glyma16g28290.1 sequence type=CDS gene model=Glyma16g28290 sequence assembly version=Glyma 1.0 annotation version=1.1 JGI Gene Call confidence=high ATGAAGTTCGAGATAGAGGACATAACCGTGTACTTCCCCTACGACAACATCTACCCGGAGCAATACTCCTACATGGTAGAACTCAAGCGCGCCCTCGACGCCAAGGGCCACTGCCTCCTAGAAATGCCCACCGGCACGGGGAAAACCATCGCACTCCTCTCCTTGATCACAAGCTACGTTCTTTCCAAACCCCATTCCCCCCTCAAGCTCCTCTACTGCACCCGCACCGTCCACGAGATGGAGAAGACGCTCGCCGAGCTCCGCCTCCTCCACGACTACCAGCTCCGCCACCTTGGCCCCGCCGCCAAGATCCTCGCCCTTGGCCTGTCGTCCAGGAAGAATCTCTGCGTTAATCCGCGGGTTCTCGCCGCGGAGAATCGCGACTCCGTGGACGCTGGATGCCGGAAGCTGACCGCGTCGTGGGTCCGGGCGGTGGCCGCGGAGAACCCTGGCGTGCCGACGTGTGAGTTCTTTGAGCAGTATGAGCGGGCGGGGTCGTCCGCGGTTCTGCCTCCCGGGGTTTATACATTGCAGGACTTGAGAGTATATGGGAAGGAGAAGGGGTGGTGCCCATACTATTTGGCACGACATATGGTGCAGTTTGCCAACGTGGTGGTGTATAGCTATCAGTATTTGCTTGATCCAAAGGTGGCTGGCATAATATCTAAGGAAATGCAGAAAGAGTCAGTTGTTGTGTTTGATGAAGCTCATAATATTGATAATGTCTGTATTGAAGCGCTTAGTGTGAGTGTGAGGAGGCAGACTATTGAAGGTGCTAGAAGAAATCTTAATAGGATGCGTCAGGAAATTGACAAGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTCGAAGGTTTGGCACTAAGAGGAGACCTGCCTGCTACTGATGCCTGGCTTGCAAATCCGGCCTTGCCTGATGATATACTAAAGGAGGCTGTACCTGGAAATATTCGCCGGGCTGAGCATTTTATTCATGTTTTGCGTAGATTAGTTCAATACCTTGAAGGGCGCTTGGATACTGAGAATGTGGAGAAGGAGAGCCCTGTTAGCTTTGTTGTTTCTATTCTTAACCATGCCGGAATTGACCAAAAAGCACTAAAGTTCTGTTATGATCGCCTTCATTCTTTGATGATGACATTGGAAATTACAGACACCGATGAGTTCCTTCATATCCAAACTATATGTGATTTTGCCACCCTTGTAGGAACATATGCTCGTGGTTTTTCTATTATAATTGAACCTTTTGATGAGCGAATGCCACATATTCCTGATCCTGTATTACAGCTTTGTTGCCATGATGCTTCTCTTGCTATCAAGCCAGTTTTTGAGCGATTTCAGTCTGTTGTGATTACATCTGGCACACTAAGCCCAATAGATTTGTACCCTCGTCTTTTGAATTTCAATCCTGTTGTCAGTAGAAGTTTTACTATGTCCTTAACAAGAGATTGCATATGTCCTATGGTGCTTACCCGTGGCAGTGATCAGCTTCCAGTCAGTACGAAATTTGATATGAGAAGTGATCTGGGTGTGGTAAGGAATTATGGAAGACTCTTGTTGGAAATGGCTTCAGTTGTTCCGGATGGGATTGTATGTTTCTTTGTTAGTTACTCATATATGGATGGGATAGTCAATACTTGGAATGAAAATGGAATTTTAAAGGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAGGTGCTATCTTTTTTTCTGTTGCTAGGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAAGATTTTGCTTGCACGTCTGGAATATCTACGGGATACTTTTCAAATTAAGGAAGGAGATTTTCTGACTTTTGATGCATTGAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAGGTATAGTCGCCATGACAAACGTTCAAAATTGCCTAGTTGGATACTATCTCACTTACATGATGCCCACCTGAACTTGAGCACAGACATGGCTTTGCATATAGCACGTGAGTTCCTCAGGAAAATGGCCCAGCCTTATGATAAAACCGGTGGCACTGGCAGGAAAACCTTGTTGTCCCAGGAAGACTTGGAGAAGATGGCTGTCAGTGGCTTGGATGATATGATGTATTGA
>Glyma16g28290.1 sequence type=predicted peptide gene model=Glyma16g28290 sequence assembly version=Glyma 1.0 annotation version=1.1 JGI Gene Call confidence=high MKFEIEDITVYFPYDNIYPEQYSYMVELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPHSPLKLLYCTRTVHEMEKTLAELRLLHDYQLRHLGPAAKILALGLSSRKNLCVNPRVLAAENRDSVDAGCRKLTASWVRAVAAENPGVPTCEFFEQYERAGSSAVLPPGVYTLQDLRVYGKEKGWCPYYLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTIEGARRNLNRMRQEIDKFKATDAGRLRAEYNRLVEGLALRGDLPATDAWLANPALPDDILKEAVPGNIRRAEHFIHVLRRLVQYLEGRLDTENVEKESPVSFVVSILNHAGIDQKALKFCYDRLHSLMMTLEITDTDEFLHIQTICDFATLVGTYARGFSIIIEPFDERMPHIPDPVLQLCCHDASLAIKPVFERFQSVVITSGTLSPIDLYPRLLNFNPVVSRSFTMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDLGVVRNYGRLLLEMASVVPDGIVCFFVSYSYMDGIVNTWNENGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAIFFSVARGKVAEGIDFDRHYGRLVIMFGVPFQYTLSKILLARLEYLRDTFQIKEGDFLTFDALRQAAQCVGRVIRSKADYGMMIFADKRYSRHDKRSKLPSWILSHLHDAHLNLSTDMALHIAREFLRKMAQPYDKTGGTGRKTLLSQEDLEKMAVSGLDDMMY*
| 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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