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Report for Sequence Feature Glyma09g03990

Feature Type:gene_model
Chromosome:Gm09
Start:2919887
stop:2926740
Source:JGI
Version:Wm82.a1.v1.1
High confidence:yes



A newer version of this gene model can be found here:

Annotations for Glyma09g03990
Database IDAnnotation TypeAnnotation DescriptionAnnotation SourceMatch ScoreEvidence Code
AT2G18790AT Annotation by Michelle Graham. TAIR10: phytochrome B | chr2:8140079-8144151 FORWARD LENGTH=1172 SoyBaseE_val: 0ISS
GO:0006325GO-bp Annotation by Michelle Graham. GO Biological Process: chromatin organization SoyBaseN/AISS
GO:0006355GO-bp Annotation by Michelle Graham. GO Biological Process: regulation of transcription, DNA-dependent SoyBaseN/AISS
GO:0007623GO-bp Annotation by Michelle Graham. GO Biological Process: circadian rhythm SoyBaseN/AISS
GO:0009409GO-bp Annotation by Michelle Graham. GO Biological Process: response to cold SoyBaseN/AISS
GO:0009630GO-bp Annotation by Michelle Graham. GO Biological Process: gravitropism SoyBaseN/AISS
GO:0009638GO-bp Annotation by Michelle Graham. GO Biological Process: phototropism SoyBaseN/AISS
GO:0009649GO-bp Annotation by Michelle Graham. GO Biological Process: entrainment of circadian clock SoyBaseN/AISS
GO:0009687GO-bp Annotation by Michelle Graham. GO Biological Process: abscisic acid metabolic process SoyBaseN/AISS
GO:0009867GO-bp Annotation by Michelle Graham. GO Biological Process: jasmonic acid mediated signaling pathway SoyBaseN/AISS
GO:0010017GO-bp Annotation by Michelle Graham. GO Biological Process: red or far-red light signaling pathway SoyBaseN/AISS
GO:0010029GO-bp Annotation by Michelle Graham. GO Biological Process: regulation of seed germination SoyBaseN/AISS
GO:0010148GO-bp Annotation by Michelle Graham. GO Biological Process: transpiration SoyBaseN/AISS
GO:0010155GO-bp Annotation by Michelle Graham. GO Biological Process: regulation of proton transport SoyBaseN/AISS
GO:0010161GO-bp Annotation by Michelle Graham. GO Biological Process: red light signaling pathway SoyBaseN/AISS
GO:0010202GO-bp Annotation by Michelle Graham. GO Biological Process: response to low fluence red light stimulus SoyBaseN/AISS
GO:0010218GO-bp Annotation by Michelle Graham. GO Biological Process: response to far red light SoyBaseN/AISS
GO:0010374GO-bp Annotation by Michelle Graham. GO Biological Process: stomatal complex development SoyBaseN/AISS
GO:0010617GO-bp Annotation by Michelle Graham. GO Biological Process: circadian regulation of calcium ion oscillation SoyBaseN/AISS
GO:0015979GO-bp Annotation by Michelle Graham. GO Biological Process: photosynthesis SoyBaseN/AISS
GO:0031347GO-bp Annotation by Michelle Graham. GO Biological Process: regulation of defense response SoyBaseN/AISS
GO:0046685GO-bp Annotation by Michelle Graham. GO Biological Process: response to arsenic-containing substance SoyBaseN/AISS
GO:0046777GO-bp Annotation by Michelle Graham. GO Biological Process: protein autophosphorylation SoyBaseN/AISS
GO:0005634GO-cc Annotation by Michelle Graham. GO Cellular Compartment: nucleus SoyBaseN/AISS
GO:0005886GO-cc Annotation by Michelle Graham. GO Cellular Compartment: plasma membrane SoyBaseN/AISS
GO:0016604GO-cc Annotation by Michelle Graham. GO Cellular Compartment: nuclear body SoyBaseN/AISS
GO:0004673GO-mf Annotation by Michelle Graham. GO Molecular Function: protein histidine kinase activity SoyBaseN/AISS
GO:0004871GO-mf Annotation by Michelle Graham. GO Molecular Function: signal transducer activity SoyBaseN/AISS
GO:0005515GO-mf Annotation by Michelle Graham. GO Molecular Function: protein binding SoyBaseN/AISS
GO:0008020GO-mf Annotation by Michelle Graham. GO Molecular Function: G-protein coupled photoreceptor activity SoyBaseN/AISS
GO:0009883GO-mf Annotation by Michelle Graham. GO Molecular Function: red or far-red light photoreceptor activity SoyBaseN/AISS
GO:0042802GO-mf Annotation by Michelle Graham. GO Molecular Function: identical protein binding SoyBaseN/AISS
PTHR24423Panther TWO COMPONENT SIGNAL TRANSDUCTION PROTEIN-RELATED JGI ISS
PF00360PFAM Phytochrome region JGI ISS
PF00512PFAM His Kinase A (phosphoacceptor) domain JGI ISS
PF00989PFAM PAS fold JGI ISS
PF01590PFAM GAF domain JGI ISS
PF02518PFAM Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase JGI ISS
PF08446PFAM PAS fold JGI ISS
UniRef100_B4YB10UniRef Annotation by Michelle Graham. Best UniRef hit: Phytochrome n=1 Tax=Glycine max RepID=B4YB10_SOYBN SoyBaseE_val: 0ISS
UniRef100_B4YB10UniRef Annotation by Michelle Graham. Most informative UniRef hit: Phytochrome n=1 Tax=Glycine max RepID=B4YB10_SOYBN SoyBaseE_val: 0ISS

Proteins Associated with Glyma09g03990
LocusGene SymbolProtein Name
PHYB1 Phytochrome B gene 1

Expression Patterns of Glyma09g03990
Gene expression representations made with eFP at the University of Toronto.
Waese et al. 2017, Plant Cell 29(8):1806-1821 ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology
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

To see more experiments click HERE

Paralogs of Glyma09g03990
ParalogEvidenceComments
Glyma15g14980 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.

Gene model name correspondences to Glyma09g03990 Gene Call Version Wm82.a1.v1.1
Corresponding NameAnnotation VersionEvidenceComments
Glyma.09g035500 Wm82.a2.v1IGC As supplied by JGI

References for Glyma09g03990
Schmutz et al. 2010
  Genome sequence of the palaeopolyploid soybean
  Nature 2010, 463:178-183

Coding sequences of Glyma09g03990
>Glyma09g03990.1   sequence type=CDS   gene model=Glyma09g03990   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGGCTTCAGCAAGCGGAGCGGCGAATTCCTCCGTTCCGCCGCCGCAAATCCACACCTCACGAACAAAGCTGAGCCACCACAGCAGCAACAACAACAACAACATCGACTCCATGAGCAAGGCCATCGCGCAGTACACGGAGGACGCGCGGCTCCACGCCGTCTTCGAGCAGTCCGGCGAGTCCGGGAGGTCCTTCAACTACTCCGAATCAATCCGCATCGCATCGGAATCCGTCCCCGAGCAGCAGATAACGGCTTACCTTGTCAAAATCCAGCGCGGCGGCTTCATCCAGCCCTTCGGCTCCATGATCGCCGTCGACGAGCCCTCCTTCCGCATCCTCGGTTACTCCGACAACGCCCGCGACATGCTCGGCATTACTCCGCAGTCCGTCCCTTCGCTCGACGACAAGAACGACGCCGCCTTCGCTCTCGGCACCGATGTCCGAGCCCTCTTCACTCACTCCAGCGCCTTACTCCTCGAAAAGGCCTTCTCCGCACGCGAAATTAGCCTCATGAACCCTATCTGGATCCACTCCAGAACCTCCGGGAAGCCTTTCTATGGAATCCTCCACCGAATTGACGTCGGAATTGTCATCGATTTGGAGCCTGCGCGTACGGAGGATCCTGCCCTCTCTATCGCTGGAGCTGTCCAGTCGCAGAAGCTCGCGGTTCGCGCGATTTCGCAGCTTCAATCTCTCCCCGGCGGTGATGTTAAGCTTCTCTGTGACACTGTTGTGGAAAGTGTTAGGGAATTGACGGGTTATGATAGGGTTATGGTTTATAAGTTTCATGAGGATGAGCATGGAGAGGTTGTTTCTGAGAGTAAGAGGCCTGATTTGGAGCCTTACATTGGATTGCATTATCCTGCTACTGATATTCCTCAGGCTTCTAGGTTTTTGTTTAAGCAAAATAGAGTTAGGATGATTGTGGATTGTCATGCTTCTGCTGTGAGGGTGGTGCAGGATGAGGCTCTTGTGCAGCCTTTGTGTTTGGTTGGGTCCACCCTTAGGGCACCTCACGGTTGTCATGCTCAGTATATGGCTAACATGGGCTCGATTGCGTCTTTGGTGATGGCAGTTATTATCAATGGGAATGACGAGGAAGGCGTTGGTGGTCGCAGTTCGATGAGGCTGTGGGGGCTTGTTGTCTGCCACCATACCTCTGCCAGGTGTATTCCTTTTCCCTTGAGGTATGCTTGTGAGTTTCTGATGCAGGCGTTTGGGCTGCAGTTGAACATGGAGCTTCAGTTGGCCGCGCAGTCGTTGGAGAAGCGGGTTTTGAGGACACAGACTCTGTTGTGTGATATGCTTCTTAGGGACTCGCCTACTGGCATTGTTACTCAGAGTCCTAGTATAATGGACTTGGTGAAGTGTGATGGGGCTGCCCTTTATTTCCAAGGGAACTATTATCCGTTGGGTGTGACTCCAACTGAAGCTCAGATTAGGGATATTATTGAGTGGTTGTTGGCCTTCCATGGAGATTCGACCGGTTTGAGTACTGATAGTCTGGGTGATGCTGGATATCCCGGGGCTGCCTCGCTTGGGGATGCAGTTTGTGGGATGGCGGTTGCTTATATTACAGAGAAGGATTTTCTTTTCTGGTTCAGGTCGCACACGGCCAAAGAGATCAAATGGGGTGGTGCAAAGCATCATCCTGAGGACAAGGATGATGGGCAGAGAATGCATCCCCGTTCTTCCTTCAAGGCGTTTTTAGAAGTGGTGAAAAGCCGTAGCTTGCCGTGGGAGAATGCGGAAATGGATGCAATTCACTCTTTGCAGCTTATTCTGCGTGACTCGTTTAAAGATGCTGAGCATAGAAATTCTAAGGCTGTTGTGGATCCCCATGTGTCAGAACAAGAGTTGCAAGGGGTGGATGAACTAAGTTCTGTGGCCAGAGAGATGGTTAGATTGATAGAAACAGCCACTGCTCCAATATTTGCTGTTGATGTCGATGGCCACGTAAATGGGTGGAATGCAAAGGTTTCAGAATTAACAGGACTCCCAGTTGAGGAGGCTATGGGGAAGTCCTTGGTTCACGATCTTGTGTTTAAGGAGTCTGAAGAAACTATGAACAAGCTTCTTTCTCGTGCTTTAAAAGGTGAAGAAGATAAGAATGTTGAGATAAAAATGAGGACGTTTGGCCCAGAACATCAAAATAAGGCAGTGTTTTTAGTGGTGAATGCTTGCTCCAGCAAGGATTTTACAAATAATGTAGTTGGAGTGTGCTTTGTTGGTCAGGATGTTACTGGTCAAAAAATTGTAATGGACAAATTCATCAACATACAAGGTGACTACAAGGCTATTGTACATAGCCCAAATCCTTTGATCCCTCCCATTTTTGCATCGGACGATAACACATGTTGCTTAGAGTGGAACACTGCAATGGAAAAGCTTACTGGTTGGGGCCGTGTGGATGTCATTGGAAAAATGTTGGTGGGAGAGGTTTTTGGTAGTTGCTGTCAGTTGAAGGGTTCAGATTCAATAACAAAGTTCATGATTGTCTTACACAATGCACTTGGTGGACAAGATACAGATAAATTCCCTTTCTCATTTCTTGATCGGCACGGAAAGTATGTACAAACTTTCCTGACTGCAAATAAGAGGGTTAACATGGAGGGTCAGATCATAGGAGCTTTTTGCTTTTTGCAAATCATGAGTCCGGAACTTCAGCAGGCTCTTAAGGCACAGAGACAACAAGAAAAGAATTCCTTTGGTAGGATGAAAGAGTTAGCTTATATTTGTCAAGGAGTTAAGAATCCTTTGAGTGGCATACGCTTTACAAACTCTCTTTTGGAGGCTACAAGCTTGACCAATGAGCAAAAGCAGTTTCTTGAGACTAGTGTTGCTTGTGAGAAGCAAATGTTAAAGATAATACGCGACGTTGATCTTGAAAGCATCGAGGATGGGTCCCTGGAGCTTGAAAAGGGGGAATTCTTGCTTGGAAATGTCATAAATGCAGTTGTTAGCCAAGTAATGTTACTGTTAAGAGAAAGAAATTTACAGTTGATTCGTGATATTCCTGAAGAAATCAAGACATTGGCAGTTTATGGTGATCAATTGAGGATTCAACAAGTGTTGTCTGATTTCTTGTTGAATATAGTGCGCTATGCACCATCTCCAGATGGCTGGGTAGAGATTCATGTACGTCCAAGAATAAAACAAATCTCAGATGGGCTCACTCTTCTCCATGCTGAATTTAGAATGGTATGTCCTGGTGAAGGTCTTCCTCCTGAATTGATTCAAGACATGTTCAATAACAGTCGGTGGGGGACTCAAGAAGGTTTAGGGCTGAGCATGAGCAGGAAGATTCTAAAGCTAATGAACGGCGAAGTGCAGTATATCAGGGAGGCCGAACGGTGCTACTTCTATGTTCTTCTTGAACTACCTGTGACACGGAGAAGCTCTAAAAAGTGTTAA
Predicted protein sequences of Glyma09g03990
>Glyma09g03990.1   sequence type=predicted peptide   gene model=Glyma09g03990   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MASASGAANSSVPPPQIHTSRTKLSHHSSNNNNNIDSMSKAIAQYTEDARLHAVFEQSGESGRSFNYSESIRIASESVPEQQITAYLVKIQRGGFIQPFGSMIAVDEPSFRILGYSDNARDMLGITPQSVPSLDDKNDAAFALGTDVRALFTHSSALLLEKAFSAREISLMNPIWIHSRTSGKPFYGILHRIDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDVKLLCDTVVESVRELTGYDRVMVYKFHEDEHGEVVSESKRPDLEPYIGLHYPATDIPQASRFLFKQNRVRMIVDCHASAVRVVQDEALVQPLCLVGSTLRAPHGCHAQYMANMGSIASLVMAVIINGNDEEGVGGRSSMRLWGLVVCHHTSARCIPFPLRYACEFLMQAFGLQLNMELQLAAQSLEKRVLRTQTLLCDMLLRDSPTGIVTQSPSIMDLVKCDGAALYFQGNYYPLGVTPTEAQIRDIIEWLLAFHGDSTGLSTDSLGDAGYPGAASLGDAVCGMAVAYITEKDFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWENAEMDAIHSLQLILRDSFKDAEHRNSKAVVDPHVSEQELQGVDELSSVAREMVRLIETATAPIFAVDVDGHVNGWNAKVSELTGLPVEEAMGKSLVHDLVFKESEETMNKLLSRALKGEEDKNVEIKMRTFGPEHQNKAVFLVVNACSSKDFTNNVVGVCFVGQDVTGQKIVMDKFINIQGDYKAIVHSPNPLIPPIFASDDNTCCLEWNTAMEKLTGWGRVDVIGKMLVGEVFGSCCQLKGSDSITKFMIVLHNALGGQDTDKFPFSFLDRHGKYVQTFLTANKRVNMEGQIIGAFCFLQIMSPELQQALKAQRQQEKNSFGRMKELAYICQGVKNPLSGIRFTNSLLEATSLTNEQKQFLETSVACEKQMLKIIRDVDLESIEDGSLELEKGEFLLGNVINAVVSQVMLLLRERNLQLIRDIPEEIKTLAVYGDQLRIQQVLSDFLLNIVRYAPSPDGWVEIHVRPRIKQISDGLTLLHAEFRMVCPGEGLPPELIQDMFNNSRWGTQEGLGLSMSRKILKLMNGEVQYIREAERCYFYVLLELPVTRRSSKKC*






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