Glyma05g02540 - SoyBase

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Report for Sequence Feature Glyma05g02540

Feature Type:	gene_model
Chromosome:	Gm05
Start:	1920325
stop:	1924779
Source:	JGI
Version:	Wm82.a1.v1.1
High confidence:	yes

A newer version of this gene model can be found here:

Annotations for Glyma05g02540

Database ID	Annotation Type	Annotation Description	Annotation Source	Match Score	Evidence Code
AT5G63110	AT	Annotation by Michelle Graham. TAIR10: histone deacetylase 6 \| chr5:25315834-25318227 REVERSE LENGTH=471	SoyBase	E_val: 0	ISS
GO:0000085	GO-bp	Annotation by Michelle Graham. GO Biological Process: G2 phase of mitotic cell cycle	SoyBase	N/A	ISS
GO:0009640	GO-bp	Annotation by Michelle Graham. GO Biological Process: photomorphogenesis	SoyBase	N/A	ISS
GO:0009651	GO-bp	Annotation by Michelle Graham. GO Biological Process: response to salt stress	SoyBase	N/A	ISS
GO:0009737	GO-bp	Annotation by Michelle Graham. GO Biological Process: response to abscisic acid stimulus	SoyBase	N/A	ISS
GO:0009793	GO-bp	Annotation by Michelle Graham. GO Biological Process: embryo development ending in seed dormancy	SoyBase	N/A	ISS
GO:0010228	GO-bp	Annotation by Michelle Graham. GO Biological Process: vegetative to reproductive phase transition of meristem	SoyBase	N/A	ISS
GO:0010431	GO-bp	Annotation by Michelle Graham. GO Biological Process: seed maturation	SoyBase	N/A	ISS
GO:0016441	GO-bp	Annotation by Michelle Graham. GO Biological Process: posttranscriptional gene silencing	SoyBase	N/A	ISS
GO:0016458	GO-bp	Annotation by Michelle Graham. GO Biological Process: gene silencing	SoyBase	N/A	ISS
GO:0016575	GO-bp	Annotation by Michelle Graham. GO Biological Process: histone deacetylation	SoyBase	N/A	ISS
GO:0005634	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: nucleus	SoyBase	N/A	ISS
GO:0009941	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: chloroplast envelope	SoyBase	N/A	ISS
GO:0004407	GO-mf	Annotation by Michelle Graham. GO Molecular Function: histone deacetylase activity	SoyBase	N/A	ISS
GO:0005515	GO-mf	Annotation by Michelle Graham. GO Molecular Function: protein binding	SoyBase	N/A	ISS
KOG1342	KOG	Histone deacetylase complex, catalytic component RPD3	JGI		ISS
PTHR10625	Panther	HISTONE DEACETYLASE	JGI		ISS
PTHR10625:SF28	Panther	HISTONE DEACETYLASE 1, 2 ,3	JGI		ISS
PTHR10625:SF65	Panther	HISTONE DEACETYLASE RPD3	JGI		ISS
PF00850	PFAM	Histone deacetylase domain	JGI		ISS
UniRef100_I1K037	UniRef	Annotation by Michelle Graham. Best UniRef hit: Histone deacetylase n=1 Tax=Glycine max RepID=I1K037_SOYBN	SoyBase	E_val: 0	ISS
UniRef100_I1K037	UniRef	Annotation by Michelle Graham. Most informative UniRef hit: Histone deacetylase n=1 Tax=Glycine max RepID=I1K037_SOYBN	SoyBase	E_val: 0	ISS

Expression Patterns of Glyma05g02540

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 Glyma05g02540

Paralog	Evidence	Comments
Glyma17g09320	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 Glyma05g02540 Gene Call Version Wm82.a1.v1.1

Corresponding Name	Annotation Version	Evidence	Comments
Glyma.05g040600	Wm82.a2.v1	IGC	As supplied by JGI

References for Glyma05g02540

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

Transcripts of Glyma05g02540

Limit To All Plant Sequences

>Glyma05g02540.2   sequence type=transcript   gene model=Glyma05g02540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATAACATTTTAAAGTAGATAAGCCTTCCCCGCCCACTAGAAATAGAGAGAAGGTAAGGAGGGTTTGGTTTTGGGTACTTTACAAATTACAATAATTAGCGAAAGAGAGAAGACATAGCACATAGAGTCATAGAGACATCATCATCGTATGGGAATGGAAGAGGAGAGTAGCAACAACAGCAGCATCATAGAAGGTGGTGCTTCGCTGCCATCAACGGGTTCAGACGCCAAGAAGCGAAGAGTGACGTACTTCTACGAGCCCACGATCGGCGATTACTACTACGGTCAGGGGCACCCAATGAAGCCGCACCGAATCCGCATGGCGCACAACCTCATCGTCCACTACTCCCTCCACCGCCGCATGGAGATCAACCGTCCCTTCCCGGCCTCCCCCGCCGACATCCGCCGCTTCCACTCCGACGACTACGTCGACTTTCTCTCCTCCGTCTCCCCCGAGACCCTCGCCGATTCCGCCTTCTCCCGCCACCTCAAGCGCTTCAACGTCGGCGAGGACTGCCCCGTCTTCGACGGCCTCTTCCCCTTCTGCCAGGCCTCCGCCGGCGGCTCCCTCGGCGCCGCCGTCAAACTCAACCGCGCCGACGCCGACATCGCCATCAATTGGGCCGGCGGCCTCCACCACGCCAAGAAGTCCGAGGCCTCTGGATTCTGCTACGTCAACGACATTGTCCTCGGTATCCTCGAACTCCTCAAAGTTCACAGGCGCGTGCTGTATGTTGACATTGATGTTCACCATGGTGATGGTGTTGAGGAGGCCTTTTACACCACTGATAGAGTGATGACAGTGTCTTTCCATAAGTTTGGGGACTTTTTCCCTGGCACAGGACACGTCAAGGACATTGGGGTGGGATCAGGAAAGAATTATGCAGTCAATGTCCCATTAAATGACGGAATGGATGATGAGAGTTTCCGTAGTCTGTTTCGAACCATCATTCAAAAAGTCATGGAGGTCTATCAACCAGAGGCAGTTGTTCTACAATGTGGAGCTGATTCATTGTCTGGGGACAGGTTGGGTTGCTTCAACTTGTCTGTGAGAGGTCATGCAGATTGCCTTCGTTTTCTTAGATCGTTCAATGTTCCTTTAATGGTCTTGGGTGGGGGTGGATATACAATTCGGAATGTTGCCCGTTGTTGGTGTTATGAGACAGCAGTGGCAGTAGGAGTGGAGCCTGATAATAAGTTGCCTTATAATGAATATTATGAATATTTTGGCCCAGATTATACTCTCTATGTCGATCCAAGCAACATGGAGAACCTAAACACACCCAAGGATATGGAAAAAATAAGGGACATTACAGATGAAATGGAAGAAGAGAAACCAGAAGTGCATCCATCATCTTGTTGTTGATAGAACAGAGCAAGTTCTTGCACAGCATGTTTGTATTGTTATCTTTATTCCGTTTATGGGGGAGATCATTACTAAACAGTACCACATGCAGCTGTTGAGAATGCAAATATAATCAATACATTGTGCAAATGTAATATAGTGTAAAACATTGTTTTGGTCTCTCTCGTAAACTATTTTTGTTTAAGTCATTTTCTTTTATTTGGTCCCTGGCTTACACTTAGTTTCGTTTTAGTCTGTCATGGTCAATTTAGTTGATTTTGAATATTCTCATTTGTGCATACTTTCATTTGGTCAAATGGATACATCACTTTAATTTGGTTCTTGTATCTTTTTCCTGTATGATGAGGATATTAAAGAAAGTGAGGAAGGTGCGAAATGTTGTTGTTTTCTTGTTACTATTTCATTTTTGAAAAATTATGT

Coding sequences of Glyma05g02540

Limit To All Plant Sequences

>Glyma05g02540.1   sequence type=CDS   gene model=Glyma05g02540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGGGAATGGAAGAGGAGAGTAGCAACAACAGCAGCATCATAGAAGGTGGTGCTTCGCTGCCATCAACGGGTTCAGACGCCAAGAAGCGAAGAGTGACGTACTTCTACGAGCCCACGATCGGCGATTACTACTACGGTCAGGGGCACCCAATGAAGCCGCACCGAATCCGCATGGCGCACAACCTCATCGTCCACTACTCCCTCCACCGCCGCATGGAGATCAACCGTCCCTTCCCGGCCTCCCCCGCCGACATCCGCCGCTTCCACTCCGACGACTACGTCGACTTTCTCTCCTCCGTCTCCCCCGAGACCCTCGCCGATTCCGCCTTCTCCCGCCACCTCAAGCGCTTCAACGTCGGCGAGGACTGCCCCGTCTTCGACGGCCTCTTCCCCTTCTGCCAGGCCTCCGCCGGCGGCTCCCTCGGCGCCGCCGTCAAACTCAACCGCGCCGACGCCGACATCGCCATCAATTGGGCCGGCGGCCTCCACCACGCCAAGAAGTCCGAGGCCTCTGGATTCTGCTACGTCAACGACATTGTCCTCGGTATCCTCGAACTCCTCAAAGTTCACAGGCGCGTGCTGTATGTTGACATTGATGTTCACCATGGTGATGGTGTTGAGGAGGCCTTTTACACCACTGATAGAGTGATGACAGTGTCTTTCCATAAGTTTGGGGACTTTTTCCCTGGCACAGGACACGTCAAGGACATTGGGGTGGGATCAGGAAAGAATTATGCAGTCAATGTCCCATTAAATGACGGAATGGATGATGAGAGTTTCCGTAGTCTGTTTCGAACCATCATTCAAAAAGTCATGGAGGTCTATCAACCAGAGGCAGTTGTTCTACAATGTGGAGCTGATTCATTGTCTGGGGACAGGTTGGGTTGCTTCAACTTGTCTGTGAGAGGTCATGCAGATTGCCTTCGTTTTCTTAGATCGTTCAATGTTCCTTTAATGGTCTTGGGTGGGGGTGGATATACAATTCGGAATGTTGCCCGTTGTTGGTGTTATGAGACAGCAGTGGCAGTAGGAGTGGAGCCTGATAATAAGTTGCCTTATAATGAATATTATGAATATTTTGGCCCAGATTATACTCTCTATGTCGATCCAAGCAACATGGAGAACCTAAACACACCCAAGGATATGGAAAAAATAAGGAACACACTACTAGAACAGATTTCTCAACTTCCCCATGCTCCCGGTGTACCTTTTCAGACAACACCACCTACCTTACAACTTCCGGAAGAGGCAGAAGAGGACATGGATAGAAGACCTAAACTTCGCAAATGGGATGGTGAAGATTATGATTCTGATCCTGATGAAGGTGGAAAGGCTAATTCCAAGTTTCCAAACGTCACTGCCCATATGAGGGACATTACAGATGAAATGGAAGAAGAGAAACCAGAAGTGCATCCATCATCTTGTTGTTGA

>Glyma05g02540.2   sequence type=CDS   gene model=Glyma05g02540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGGGAATGGAAGAGGAGAGTAGCAACAACAGCAGCATCATAGAAGGTGGTGCTTCGCTGCCATCAACGGGTTCAGACGCCAAGAAGCGAAGAGTGACGTACTTCTACGAGCCCACGATCGGCGATTACTACTACGGTCAGGGGCACCCAATGAAGCCGCACCGAATCCGCATGGCGCACAACCTCATCGTCCACTACTCCCTCCACCGCCGCATGGAGATCAACCGTCCCTTCCCGGCCTCCCCCGCCGACATCCGCCGCTTCCACTCCGACGACTACGTCGACTTTCTCTCCTCCGTCTCCCCCGAGACCCTCGCCGATTCCGCCTTCTCCCGCCACCTCAAGCGCTTCAACGTCGGCGAGGACTGCCCCGTCTTCGACGGCCTCTTCCCCTTCTGCCAGGCCTCCGCCGGCGGCTCCCTCGGCGCCGCCGTCAAACTCAACCGCGCCGACGCCGACATCGCCATCAATTGGGCCGGCGGCCTCCACCACGCCAAGAAGTCCGAGGCCTCTGGATTCTGCTACGTCAACGACATTGTCCTCGGTATCCTCGAACTCCTCAAAGTTCACAGGCGCGTGCTGTATGTTGACATTGATGTTCACCATGGTGATGGTGTTGAGGAGGCCTTTTACACCACTGATAGAGTGATGACAGTGTCTTTCCATAAGTTTGGGGACTTTTTCCCTGGCACAGGACACGTCAAGGACATTGGGGTGGGATCAGGAAAGAATTATGCAGTCAATGTCCCATTAAATGACGGAATGGATGATGAGAGTTTCCGTAGTCTGTTTCGAACCATCATTCAAAAAGTCATGGAGGTCTATCAACCAGAGGCAGTTGTTCTACAATGTGGAGCTGATTCATTGTCTGGGGACAGGTTGGGTTGCTTCAACTTGTCTGTGAGAGGTCATGCAGATTGCCTTCGTTTTCTTAGATCGTTCAATGTTCCTTTAATGGTCTTGGGTGGGGGTGGATATACAATTCGGAATGTTGCCCGTTGTTGGTGTTATGAGACAGCAGTGGCAGTAGGAGTGGAGCCTGATAATAAGTTGCCTTATAATGAATATTATGAATATTTTGGCCCAGATTATACTCTCTATGTCGATCCAAGCAACATGGAGAACCTAAACACACCCAAGGATATGGAAAAAATAAGGGACATTACAGATGAAATGGAAGAAGAGAAACCAGAAGTGCATCCATCATCTTGTTGTTGA

Predicted protein sequences of Glyma05g02540

Limit To All Plant Sequences

>Glyma05g02540.1   sequence type=predicted peptide   gene model=Glyma05g02540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MGMEEESSNNSSIIEGGASLPSTGSDAKKRRVTYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYSLHRRMEINRPFPASPADIRRFHSDDYVDFLSSVSPETLADSAFSRHLKRFNVGEDCPVFDGLFPFCQASAGGSLGAAVKLNRADADIAINWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKFGDFFPGTGHVKDIGVGSGKNYAVNVPLNDGMDDESFRSLFRTIIQKVMEVYQPEAVVLQCGADSLSGDRLGCFNLSVRGHADCLRFLRSFNVPLMVLGGGGYTIRNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLYVDPSNMENLNTPKDMEKIRNTLLEQISQLPHAPGVPFQTTPPTLQLPEEAEEDMDRRPKLRKWDGEDYDSDPDEGGKANSKFPNVTAHMRDITDEMEEEKPEVHPSSCC*

>Glyma05g02540.2   sequence type=predicted peptide   gene model=Glyma05g02540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MGMEEESSNNSSIIEGGASLPSTGSDAKKRRVTYFYEPTIGDYYYGQGHPMKPHRIRMAHNLIVHYSLHRRMEINRPFPASPADIRRFHSDDYVDFLSSVSPETLADSAFSRHLKRFNVGEDCPVFDGLFPFCQASAGGSLGAAVKLNRADADIAINWAGGLHHAKKSEASGFCYVNDIVLGILELLKVHRRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKFGDFFPGTGHVKDIGVGSGKNYAVNVPLNDGMDDESFRSLFRTIIQKVMEVYQPEAVVLQCGADSLSGDRLGCFNLSVRGHADCLRFLRSFNVPLMVLGGGGYTIRNVARCWCYETAVAVGVEPDNKLPYNEYYEYFGPDYTLYVDPSNMENLNTPKDMEKIRDITDEMEEEKPEVHPSSCC*

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