Glyma04g06540 - SoyBase

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Report for Sequence Feature Glyma04g06540

Feature Type:	gene_model
Chromosome:	Gm04
Start:	4974970
stop:	4984795
Source:	JGI
Version:	Wm82.a1.v1.1
High confidence:	yes

A newer version of this gene model can be found here:

Annotations for Glyma04g06540

Database ID	Annotation Type	Annotation Description	Annotation Source	Match Score	Evidence Code
AT5G25150	AT	Annotation by Michelle Graham. TAIR10: TBP-associated factor 5 \| chr5:8677117-8682058 FORWARD LENGTH=669	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: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:0007062	GO-bp	Annotation by Michelle Graham. GO Biological Process: sister chromatid cohesion	SoyBase	N/A	ISS
GO:0007131	GO-bp	Annotation by Michelle Graham. GO Biological Process: reciprocal meiotic recombination	SoyBase	N/A	ISS
GO:0033044	GO-bp	Annotation by Michelle Graham. GO Biological Process: regulation of chromosome organization	SoyBase	N/A	ISS
GO:0042138	GO-bp	Annotation by Michelle Graham. GO Biological Process: meiotic DNA double-strand break formation	SoyBase	N/A	ISS
GO:0045132	GO-bp	Annotation by Michelle Graham. GO Biological Process: meiotic chromosome segregation	SoyBase	N/A	ISS
GO:0005634	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: nucleus	SoyBase	N/A	ISS
GO:0000166	GO-mf	Annotation by Michelle Graham. GO Molecular Function: nucleotide binding	SoyBase	N/A	ISS
KOG0263	KOG	Transcription initiation factor TFIID, subunit TAF5 (also component of histone acetyltransferase SAGA)	JGI		ISS
PTHR19879	Panther	WD40 REPEAT PROTEIN	JGI		ISS
PF00400	PFAM	WD domain, G-beta repeat	JGI		ISS
PF04494	PFAM	WD40 associated region in TFIID subunit	JGI		ISS
UniRef100_G7J9V2	UniRef	Annotation by Michelle Graham. Most informative UniRef hit: Transcription initiation factor TFIID subunit n=1 Tax=Medicago truncatula RepID=G7J9V2_MEDTR	SoyBase	E_val: 0	ISS
UniRef100_I1JU70	UniRef	Annotation by Michelle Graham. Best UniRef hit: Uncharacterized protein n=1 Tax=Glycine max RepID=I1JU70_SOYBN	SoyBase	E_val: 0	ISS

Expression Patterns of Glyma04g06540

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 Glyma04g06540

Paralog	Evidence	Comments
Glyma06g06570	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 Glyma04g06540 Gene Call Version Wm82.a1.v1.1

Corresponding Name	Annotation Version	Evidence	Comments
Glyma.04g061600	Wm82.a2.v1	IGC	As supplied by JGI

References for Glyma04g06540

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

Transcripts of Glyma04g06540

Limit To All Plant Sequences

>Glyma04g06540.2   sequence type=transcript   gene model=Glyma04g06540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
TTTGAATACAATTGCCGTTATTTCTCTTTCAGAAAGGGTTATCCATAAAACAACAACTTAATAAAAAAAAAGAGAGAAAACAGCCCTGCACGTCGACCCAACCTCACTGGAGTTGCGTAGTTGGAATAGAACAATGGCAAAGACGACACAAATGGAGACAAAGAGGAACAAACGAAAGTTTGTGAGATGATTAAGCGTGGACGCAAACAGAGACGAAGAGAAAACACAGTAAGAATCAAATTAGGAGGTGCAGAATTCAAATCCCAAAAGAGGAAATGTATAATATGAAAATGGTAGTTTGGGGATATTTAAAAATTGGGAGGTAGAGGATTCAAATTCCAAGAGTAAAGTAAGTAAAAGGCCAAGGCCATATAACAGATCTGATTCCAGAAATAGCCCCCAGGAAGAATCAAATTTCTTGTACCCGCGAGCGAGGCAGTGGAAGAAGAAAGGGGTTTTTGATTCTGAGATCAAAGAAAGAATGGAGGACGACAAAATAGTTGGATACGTTACAGCATTCCTTAAGAAGAAAGGCTTCACGCAAACCGAGAAGATTTTCCAAGAAGAATTCCAACACAACAAATCCAACACTTCCAATTCACTTCTCGAACCCGACATTGCCAACCACCTCCTCGCCTTCTCTCAATTGGAGACTGGTCCTGCTAGGTTCCACGACGGCTACAGCAGACTAAGAACATGGACTTATTCTTCACTCGATTTGTACAAGCACGAGTTGCTCCGCGTACTTTATCCTGTGTTTATCCACTGCTTTATGGATCTTGTCGCCAAAGGACACGTTCAAGAAGCTCGGAACTTCTTCAATACTTTCCGCGAAGACCATGAAATGATGCACTTGCGTGACCTTCAGAAGTTGGAAGGAGTTCTTTCTCCTAACCATCTTGAGGAAATGGAATTCGCTCACTCGCTTAGAAAGAGCAAATTCAACATAAAGATATGTGAGTATTCCTATGAGCTTCTGTTGCAACATCTACACAGTACGCAATCCACCACTATACTTGGTATTATCAATGAGCATATTAACTTTCAAGTAACCCCTGGACAACCTAGCTTAATTTCCGATGACCCGGAAGCTGTTACCCTAACTGGAAGCAGCCAGGAAGCAGCAAACCTGATAAATCAAAAAGAAATTCATTGGGGGTTGCTTGAAGACTCTCTTGAAGAACGGCTGGAGAAGGCCGGGGCCTTGCTTTTAGACTCTGAAAAGGGTGAAGGGGAAGCAAAAGAGGGGGAGAATGATGAGACTAAGAAAAGATCCATTGAAGGAGGAAAGCAAGGTGGTGCTTCAGTCAAAAAAGTAAAAAAGGACAAGGGTGGAAGTGCAACTGGGAAAAGTGCTAAACCAGAAGCTAGCACTGTACCTGCAGCTCCTCGAGTTAAGCCAGAACTCCCCTTGCCCGTAATCCCAACTGAAGTGGAACAGTCCGTCCTGGAGGATTTAAGGAACCGTGTACAGCTTAGCAGTGTTGCATTGCCATCAGTTAGCTTTTACACATTTATCAATACACATAATGGTTTAAGCTGTTCATCAATATCCCATGACGGATCATTGATTGCTGGAGGATTTTCTGACTCATCACTGAAGGTTTGGGATATGGCAAAGCTTGGACAACAGGCCAGTTCTCTTTCGCAGGGTGAGAATGACACATCACAAAATGAACAAATATTTGGGCAAGGTGGTGGGAAAAGACAGTATACATTGTTTCAAGGTCATTCAGGGCCTGTTTATGCAGCCTCTTTTAGTCCTGTCGGGGATTTTATCCTTTCATCCTCAGCAGACTCAACAATTCGATTATGGAGCACAAAACTTAATGCCAATCTTGTTTGTTATAAGGGTCACAATTACCCTGTCTGGGATGTTCAGTTTAGTCCTGTAGGGCATTATTTTGCCAGCTCGTCACATGACAGAACTGCTAGGATTTGGTCCATGGACAGGATACAGCCCTTAAGAATAATGGCAGGGCACTTGTCTGATGTTGATTGTGTGCAATGGCATGCCAACTGCAACTACATTGCAACTGGTTCCAGTGATAAAACAGTTCGACTATGGGATGTGCAGAGTGGTGAGTGTGTCCGGGTTTTCGTTGGTCACAGGGTTATGATTTTGTCTTTGGCAATGTCTCCTGATGGTCGCTATATGGCATCTGGCGATGAAGATGGCACGATCATGATGTGGGACCTCTCTAGTGGCCGCTGTCTAACACCTTTGATTGGCCACACATCATGTGTCTGGTCCCTTGCTTTCAGGTGATCCCTACTGCACTACTTTATCATAATTAGTAAGGAGATTAATGGTTTTTAAGT

Coding sequences of Glyma04g06540

Limit To All Plant Sequences

>Glyma04g06540.1   sequence type=CDS   gene model=Glyma04g06540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGGAGGACGACAAAATAGTTGGATACGTTACAGCATTCCTTAAGAAGAAAGGCTTCACGCAAACCGAGAAGATTTTCCAAGAAGAATTCCAACACAACAAATCCAACACTTCCAATTCACTTCTCGAACCCGACATTGCCAACCACCTCCTCGCCTTCTCTCAATTGGAGACTGGTCCTGCTAGGTTCCACGACGGCTACAGCAGACTAAGAACATGGACTTATTCTTCACTCGATTTGTACAAGCACGAGTTGCTCCGCGTACTTTATCCTGTGTTTATCCACTGCTTTATGGATCTTGTCGCCAAAGGACACGTTCAAGAAGCTCGGAACTTCTTCAATACTTTCCGCGAAGACCATGAAATGATGCACTTGCGTGACCTTCAGAAGTTGGAAGGAGTTCTTTCTCCTAACCATCTTGAGGAAATGGAATTCGCTCACTCGCTTAGAAAGAGCAAATTCAACATAAAGATATGTGAGTATTCCTATGAGCTTCTGTTGCAACATCTACACAGTACGCAATCCACCACTATACTTGGTATTATCAATGAGCATATTAACTTTCAAGTAACCCCTGGACAACCTAGCTTAATTTCCGATGACCCGGAAGCTGTTACCCTAACTGGAAGCAGCCAGGAAGCAGCAAACCTGATAAATCAAAAAGAAATTCATTGGGGGTTGCTTGAAGACTCTCTTGAAGAACGGCTGGAGAAGGCCGGGGCCTTGCTTTTAGACTCTGAAAAGGGTGAAGGGGAAGCAAAAGAGGGGGAGAATGATGAGACTAAGAAAAGATCCATTGAAGGAGGAAAGCAAGGTGGTGCTTCAGTCAAAAAAGTAAAAAAGGACAAGGGTGGAAGTGCAACTGGGAAAAGTGCTAAACCAGAAGCTAGCACTGTACCTGCAGCTCCTCGAGTTAAGCCAGAACTCCCCTTGCCCGTAATCCCAACTGAAGTGGAACAGTCCGTCCTGGAGGATTTAAGGAACCGTGTACAGCTTAGCAGTGTTGCATTGCCATCAGTTAGCTTTTACACATTTATCAATACACATAATGGTTTAAGCTGTTCATCAATATCCCATGACGGATCATTGATTGCTGGAGGATTTTCTGACTCATCACTGAAGGTTTGGGATATGGCAAAGCTTGGACAACAGGCCAGTTCTCTTTCGCAGGGTGAGAATGACACATCACAAAATGAACAAATATTTGGGCAAGGTGGTGGGAAAAGACAGTATACATTGTTTCAAGGTCATTCAGGGCCTGTTTATGCAGCCTCTTTTAGTCCTGTCGGGGATTTTATCCTTTCATCCTCAGCAGACTCAACAATTCGATTATGGAGCACAAAACTTAATGCCAATCTTGTTTGTTATAAGGGTCACAATTACCCTGTCTGGGATGTTCAGTTTAGTCCTGTAGGGCATTATTTTGCCAGCTCGTCACATGACAGAACTGCTAGGATTTGGTCCATGGACAGGATACAGCCCTTAAGAATAATGGCAGGGCACTTGTCTGATGTTGATTGTGTGCAATGGCATGCCAACTGCAACTACATTGCAACTGGTTCCAGTGATAAAACAGTTCGACTATGGGATGTGCAGAGTGGTGAGTGTGTCCGGGTTTTCGTTGGTCACAGGGTTATGATTTTGTCTTTGGCAATGTCTCCTGATGGTCGCTATATGGCATCTGGCGATGAAGATGGCACGATCATGATGTGGGACCTCTCTAGTGGCCGCTGTCTAACACCTTTGATTGGCCACACATCATGTGTCTGGTCCCTTGCTTTCAGTTCTGAAGGTTCTATTATAGCATCTGGATCTGCTGATTGCACTGTAAAATTGTGGGATGTAAATGCGAGCACCAAGGTTTCTAGGGCTGAAGAAAAAAGTGGGAGTGCTAACAGCAGACTTAGATCGCTGAAAACTTTGTCAACCAAATCTACTCCAGTTTACTCATTACGGTTTTCTCGAAGGAATCTTCTTTTTGCGGCTGGCGCTCTATCAAAAAGTGGTTAA

>Glyma04g06540.2   sequence type=CDS   gene model=Glyma04g06540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGGAGGACGACAAAATAGTTGGATACGTTACAGCATTCCTTAAGAAGAAAGGCTTCACGCAAACCGAGAAGATTTTCCAAGAAGAATTCCAACACAACAAATCCAACACTTCCAATTCACTTCTCGAACCCGACATTGCCAACCACCTCCTCGCCTTCTCTCAATTGGAGACTGGTCCTGCTAGGTTCCACGACGGCTACAGCAGACTAAGAACATGGACTTATTCTTCACTCGATTTGTACAAGCACGAGTTGCTCCGCGTACTTTATCCTGTGTTTATCCACTGCTTTATGGATCTTGTCGCCAAAGGACACGTTCAAGAAGCTCGGAACTTCTTCAATACTTTCCGCGAAGACCATGAAATGATGCACTTGCGTGACCTTCAGAAGTTGGAAGGAGTTCTTTCTCCTAACCATCTTGAGGAAATGGAATTCGCTCACTCGCTTAGAAAGAGCAAATTCAACATAAAGATATGTGAGTATTCCTATGAGCTTCTGTTGCAACATCTACACAGTACGCAATCCACCACTATACTTGGTATTATCAATGAGCATATTAACTTTCAAGTAACCCCTGGACAACCTAGCTTAATTTCCGATGACCCGGAAGCTGTTACCCTAACTGGAAGCAGCCAGGAAGCAGCAAACCTGATAAATCAAAAAGAAATTCATTGGGGGTTGCTTGAAGACTCTCTTGAAGAACGGCTGGAGAAGGCCGGGGCCTTGCTTTTAGACTCTGAAAAGGGTGAAGGGGAAGCAAAAGAGGGGGAGAATGATGAGACTAAGAAAAGATCCATTGAAGGAGGAAAGCAAGGTGGTGCTTCAGTCAAAAAAGTAAAAAAGGACAAGGGTGGAAGTGCAACTGGGAAAAGTGCTAAACCAGAAGCTAGCACTGTACCTGCAGCTCCTCGAGTTAAGCCAGAACTCCCCTTGCCCGTAATCCCAACTGAAGTGGAACAGTCCGTCCTGGAGGATTTAAGGAACCGTGTACAGCTTAGCAGTGTTGCATTGCCATCAGTTAGCTTTTACACATTTATCAATACACATAATGGTTTAAGCTGTTCATCAATATCCCATGACGGATCATTGATTGCTGGAGGATTTTCTGACTCATCACTGAAGGTTTGGGATATGGCAAAGCTTGGACAACAGGCCAGTTCTCTTTCGCAGGGTGAGAATGACACATCACAAAATGAACAAATATTTGGGCAAGGTGGTGGGAAAAGACAGTATACATTGTTTCAAGGTCATTCAGGGCCTGTTTATGCAGCCTCTTTTAGTCCTGTCGGGGATTTTATCCTTTCATCCTCAGCAGACTCAACAATTCGATTATGGAGCACAAAACTTAATGCCAATCTTGTTTGTTATAAGGGTCACAATTACCCTGTCTGGGATGTTCAGTTTAGTCCTGTAGGGCATTATTTTGCCAGCTCGTCACATGACAGAACTGCTAGGATTTGGTCCATGGACAGGATACAGCCCTTAAGAATAATGGCAGGGCACTTGTCTGATGTTGATTGTGTGCAATGGCATGCCAACTGCAACTACATTGCAACTGGTTCCAGTGATAAAACAGTTCGACTATGGGATGTGCAGAGTGGTGAGTGTGTCCGGGTTTTCGTTGGTCACAGGGTTATGATTTTGTCTTTGGCAATGTCTCCTGATGGTCGCTATATGGCATCTGGCGATGAAGATGGCACGATCATGATGTGGGACCTCTCTAGTGGCCGCTGTCTAACACCTTTGATTGGCCACACATCATGTGTCTGGTCCCTTGCTTTCAGGTGA

Predicted protein sequences of Glyma04g06540

Limit To All Plant Sequences

>Glyma04g06540.1   sequence type=predicted peptide   gene model=Glyma04g06540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MEDDKIVGYVTAFLKKKGFTQTEKIFQEEFQHNKSNTSNSLLEPDIANHLLAFSQLETGPARFHDGYSRLRTWTYSSLDLYKHELLRVLYPVFIHCFMDLVAKGHVQEARNFFNTFREDHEMMHLRDLQKLEGVLSPNHLEEMEFAHSLRKSKFNIKICEYSYELLLQHLHSTQSTTILGIINEHINFQVTPGQPSLISDDPEAVTLTGSSQEAANLINQKEIHWGLLEDSLEERLEKAGALLLDSEKGEGEAKEGENDETKKRSIEGGKQGGASVKKVKKDKGGSATGKSAKPEASTVPAAPRVKPELPLPVIPTEVEQSVLEDLRNRVQLSSVALPSVSFYTFINTHNGLSCSSISHDGSLIAGGFSDSSLKVWDMAKLGQQASSLSQGENDTSQNEQIFGQGGGKRQYTLFQGHSGPVYAASFSPVGDFILSSSADSTIRLWSTKLNANLVCYKGHNYPVWDVQFSPVGHYFASSSHDRTARIWSMDRIQPLRIMAGHLSDVDCVQWHANCNYIATGSSDKTVRLWDVQSGECVRVFVGHRVMILSLAMSPDGRYMASGDEDGTIMMWDLSSGRCLTPLIGHTSCVWSLAFSSEGSIIASGSADCTVKLWDVNASTKVSRAEEKSGSANSRLRSLKTLSTKSTPVYSLRFSRRNLLFAAGALSKSG*

>Glyma04g06540.2   sequence type=predicted peptide   gene model=Glyma04g06540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MEDDKIVGYVTAFLKKKGFTQTEKIFQEEFQHNKSNTSNSLLEPDIANHLLAFSQLETGPARFHDGYSRLRTWTYSSLDLYKHELLRVLYPVFIHCFMDLVAKGHVQEARNFFNTFREDHEMMHLRDLQKLEGVLSPNHLEEMEFAHSLRKSKFNIKICEYSYELLLQHLHSTQSTTILGIINEHINFQVTPGQPSLISDDPEAVTLTGSSQEAANLINQKEIHWGLLEDSLEERLEKAGALLLDSEKGEGEAKEGENDETKKRSIEGGKQGGASVKKVKKDKGGSATGKSAKPEASTVPAAPRVKPELPLPVIPTEVEQSVLEDLRNRVQLSSVALPSVSFYTFINTHNGLSCSSISHDGSLIAGGFSDSSLKVWDMAKLGQQASSLSQGENDTSQNEQIFGQGGGKRQYTLFQGHSGPVYAASFSPVGDFILSSSADSTIRLWSTKLNANLVCYKGHNYPVWDVQFSPVGHYFASSSHDRTARIWSMDRIQPLRIMAGHLSDVDCVQWHANCNYIATGSSDKTVRLWDVQSGECVRVFVGHRVMILSLAMSPDGRYMASGDEDGTIMMWDLSSGRCLTPLIGHTSCVWSLAFR*

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