Glyma11g19840 - SoyBase

SoyBase SoyBase transitions to NEW site on 10/1/2024
Integrating Genetics and Genomics to Advance Soybean Research

Warning: Undefined variable $sxsome in /var/www/html/include/SeqFeatClass.php on line 665

Warning: Undefined variable $sstart in /var/www/html/include/SeqFeatClass.php on line 665

Warning: Undefined variable $send in /var/www/html/include/SeqFeatClass.php on line 665

Warning: get_headers(): php_network_getaddresses: getaddrinfo for bar.utoronto.ca failed: Temporary failure in name resolution in /var/www/html/include/SeqFeatClass.php on line 1018

Warning: get_headers(https://bar.utoronto.ca/api/efp_image/efp_soybean/soybean/Absolute/Glyma11g19840): Failed to open stream: php_network_getaddresses: getaddrinfo for bar.utoronto.ca failed: Temporary failure in name resolution in /var/www/html/include/SeqFeatClass.php on line 1018

Warning: Trying to access array offset on false in /var/www/html/include/SeqFeatClass.php on line 1019

Warning: get_headers(): php_network_getaddresses: getaddrinfo for bar.utoronto.ca failed: Temporary failure in name resolution in /var/www/html/include/SeqFeatClass.php on line 1020

Warning: get_headers(https://bar.utoronto.ca/api/efp_image/efp_soybean/soybean_severin/Absolute/Glyma11g19840): Failed to open stream: php_network_getaddresses: getaddrinfo for bar.utoronto.ca failed: Temporary failure in name resolution in /var/www/html/include/SeqFeatClass.php on line 1020

Warning: Trying to access array offset on false in /var/www/html/include/SeqFeatClass.php on line 1021

Deprecated: preg_match(): Passing null to parameter #2 ($subject) of type string is deprecated in /var/www/html/include/SeqFeatClass.php on line 1025

Deprecated: preg_match(): Passing null to parameter #2 ($subject) of type string is deprecated in /var/www/html/include/SeqFeatClass.php on line 1031

Report for Sequence Feature Glyma11g19840

Feature Type:	gene_model
Chromosome:	Gm11
Start:	16619910
stop:	16623705
Source:	JGI
Version:	Wm82.a1.v1.1
High confidence:	yes

A newer version of this gene model can be found here:

Annotations for Glyma11g19840

Database ID	Annotation Type	Annotation Description	Annotation Source	Match Score	Evidence Code
AT2G28190	AT	Annotation by Michelle Graham. TAIR10: copper/zinc superoxide dismutase 2 \| chr2:12014548-12016303 FORWARD LENGTH=216	SoyBase	E_val: 1.00E-93	ISS
GO:0006979	GO-bp	Annotation by Michelle Graham. GO Biological Process: response to oxidative stress	SoyBase	N/A	ISS
GO:0009407	GO-bp	Annotation by Michelle Graham. GO Biological Process: toxin catabolic process	SoyBase	N/A	ISS
GO:0009416	GO-bp	Annotation by Michelle Graham. GO Biological Process: response to light stimulus	SoyBase	N/A	ISS
GO:0010039	GO-bp	Annotation by Michelle Graham. GO Biological Process: response to iron ion	SoyBase	N/A	ISS
GO:0019430	GO-bp	Annotation by Michelle Graham. GO Biological Process: removal of superoxide radicals	SoyBase	N/A	ISS
GO:0034599	GO-bp	Annotation by Michelle Graham. GO Biological Process: cellular response to oxidative stress	SoyBase	N/A	ISS
GO:0035195	GO-bp	Annotation by Michelle Graham. GO Biological Process: gene silencing by miRNA	SoyBase	N/A	ISS
GO:0046688	GO-bp	Annotation by Michelle Graham. GO Biological Process: response to copper ion	SoyBase	N/A	ISS
GO:0071329	GO-bp	Annotation by Michelle Graham. GO Biological Process: cellular response to sucrose stimulus	SoyBase	N/A	ISS
GO:0071457	GO-bp	Annotation by Michelle Graham. GO Biological Process: cellular response to ozone	SoyBase	N/A	ISS
GO:0071472	GO-bp	Annotation by Michelle Graham. GO Biological Process: cellular response to salt stress	SoyBase	N/A	ISS
GO:0071484	GO-bp	Annotation by Michelle Graham. GO Biological Process: cellular response to light intensity	SoyBase	N/A	ISS
GO:0071493	GO-bp	Annotation by Michelle Graham. GO Biological Process: cellular response to UV-B	SoyBase	N/A	ISS
GO:0009507	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: chloroplast	SoyBase	N/A	ISS
GO:0009570	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: chloroplast stroma	SoyBase	N/A	ISS
GO:0009579	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: thylakoid	SoyBase	N/A	ISS
GO:0048046	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: apoplast	SoyBase	N/A	ISS
GO:0004784	GO-mf	Annotation by Michelle Graham. GO Molecular Function: superoxide dismutase activity	SoyBase	N/A	ISS
GO:0005507	GO-mf	Annotation by Michelle Graham. GO Molecular Function: copper ion binding	SoyBase	N/A	ISS
GO:0008270	GO-mf	Annotation by Michelle Graham. GO Molecular Function: zinc ion binding	SoyBase	N/A	ISS
GO:0046872	GO-mf	Annotation by Michelle Graham. GO Molecular Function: metal ion binding	SoyBase	N/A	ISS
KOG0441	KOG	Cu2+/Zn2+ superoxide dismutase SOD1	JGI		ISS
PTHR10003	Panther	CU/ZN SUPEROXIDE DISMUTASE	JGI		ISS
PF00080	PFAM	Copper/zinc superoxide dismutase (SODC)	JGI		ISS
UniRef100_I1LKZ2	UniRef	Annotation by Michelle Graham. Best UniRef hit: Superoxide dismutase [Cu-Zn] n=1 Tax=Glycine max RepID=I1LKZ2_SOYBN	SoyBase	E_val: 3.00E-149	ISS
UniRef100_I1LKZ2	UniRef	Annotation by Michelle Graham. Most informative UniRef hit: Superoxide dismutase [Cu-Zn] n=1 Tax=Glycine max RepID=I1LKZ2_SOYBN	SoyBase	E_val: 3.00E-149	ISS

Expression Patterns of Glyma11g19840

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

Glyma11g19840 not represented in the dataset	Glyma11g19840 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

To see more experiments click HERE

Paralogs of Glyma11g19840

Paralog	Evidence	Comments
Glyma12g08650	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 Glyma11g19840 Gene Call Version Wm82.a1.v1.1

Corresponding Name	Annotation Version	Evidence	Comments
Glyma.11g192700	Wm82.a2.v1	IGC	As supplied by JGI

References for Glyma11g19840

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

Transcripts of Glyma11g19840

Limit To All Plant Sequences

>Glyma11g19840.2   sequence type=transcript   gene model=Glyma11g19840   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
GAGTGTGAGTAAGCAGTGGCGCTTTGAGTGAGGATTATATAATTTGTTTTCACCACCAAACCAACCACAAATTCACACATTTTTTGTTGCATTATCACAAACACCTCGTCCCTCACAATGCAGCTAGCAATGGCGGCCAACGCTGTCGTTTCACCGTCGCCGTTCCGACCTCAGCCCTTTCTCCGGTCATCCTTCTCCGGCGTCTCCGTCAAGCTCACTCCCCAATCCATAACGCTTTCACGCTCCAAGCCCCTCACCGTCTTCGCCGCCACCAAGAAGGCCGTCGCCGTCCTCAAGGGGACCTCCGCCGTCGAAGGCGTCGCCACTCTCATCCAAGAAGACGATGGCCCGACGACAGTTTCTGTTCGCATCACTGGCCTTACTCCGGGGCTTCATGGTTTTCACCTACATGAGTATGGTGATACGACAAATGGGTGTATTTCTACGGGAGCACATTTTAATCCTAATAAATTGACACATGGTGCTCCTGAGGATGAAGTCCGTCATGCGGGTGACCTGGGAAACATAGTTGCTAATGCAGAGGGGGTTGCAGAGGCTACAATTGTGGATAATCAGATACCACTCTCTGGCCCCAATTCAGTAGTTGGAAGAGCCTTGGTGGTCCATGAGCTTGAGGATGACCTTGGAAAGGGTGGGCATGAACTCAGTTTGACAACTGGAAATGCTGGTGGAAGATTAGCATGTGGTGTGGTTGGTTTGACTCCAGCATAATCAGTGCAGCGAATTTTTTGTAGCAGTCGTGTTATGTTATCAGATATTATGTTCTCTGTGAAGCATGATGACTCACTGTTTTCTTCAGTTACCAATGTAAACTGTAAAGCATAATGTCCTTCTAAAGATGAGTGTGCAAATGAATCATGAAAACATGTTGTTAGTCCTTTACTGGAGATTCATCGTGCAGTCGGGTCTGTACTCCCCAATAAAATTCATCATGCAGTCAGATGTTTATTCCCCAATGAAATTGATTGCTGTAGTCCTTGTTGTCTGCTTGAGAAAGAACCTATGTTGATATTTTATATTAATGGTACAAGTGCAACGACTGGTTACTTGTTTCTAACTGT

>Glyma11g19840.3   sequence type=transcript   gene model=Glyma11g19840   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
GAGTGTGAGTAAGCAGTGGCGCTTTGAGTGAGGATTATATAATTTGTTTTCACCACCAAACCAACCACAAATTCACACATTTTTTGTTGCATTATCACAAACACCTCGTCCCTCACAATGCAGCTAGCAATGGCGGCCAACGCTGTCGTTTCACCGTCGCCGTTCCGACCTCAGCCCTTTCTCCGGTCATCCTTCTCCGGCGTCTCCGTCAAGCTCACTCCCCAATCCATAACGCTTTCACGCTCCAAGCCCCTCACCGTCTTCGCCGCCACCAAGAAGGCCGTCGCCGTCCTCAAGGGGACCTCCGCCGTCGAAGGCGTCGCCACTCTCATCCAAGAAGACGATGGCCCGACGACAGTTTCTGTTCGCATCACTGGCCTTACTCCGGGGCTTCATGGTTTTCACCTACATGAGTATGGTGATACGACAAATGGGTGTATTTCTACGGGAGCACATTTTAATCCTAATAAATTGACACATGGTGCTCCTGAGGATGAAGTCCGTCATGCGGGTGACCTGGGAAACATAGTTGCTAATGCAGAGGGGGTTGCAGAGGCTACAATTGTGGATAATCAGATACCACTCTCTGGCCCCAATTCAGTAGTTGGAAGAGCCTTGGTGGTCCATGAGCTTGAGGATGACCTTGGAAAGGGTGGGCATGAACTCAGTTTGACAACTGGAAATGCTGGTGGAAGATTAGCATGTGTGGTTGGTTTGACTCCAGCATAATCAGTGCAGCGAATTTTTTGTAGCAGTCGTGTTATGTTATCAGATATTATGTTCTCTGTGAAGCATGATGACTCACTGTTTTCTTCAGTTACCAATGTAAACTGTAAAGCATAATGTCCTTCTAAAGATGAGTGTGCAAATGAATCATGAAAACATGTTGTTAGTCCTTTACTGGAGATTCATCGTGCAGTCGGGTCTGTACTCCCCAATAAAATTCATCATGCAGTCAGATGTTTATTCCCCAATGAAATTGATTGCTGTAGTCCTTGTTGTCTGCTTGAGAAAGAACCTATGTTGATATTTTATATTAATGGTACAAGTGCAACGACTGGTTACTTGTTTCTAACTGT

Coding sequences of Glyma11g19840

Limit To All Plant Sequences

>Glyma11g19840.1   sequence type=CDS   gene model=Glyma11g19840   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGCAGCTAGCAATGGCGGCCAACGCTGTCGTTTCACCGTCGCCGTTCCGACCTCAGCCCTTTCTCCGGTCATCCTTCTCCGGCGTCTCCGTCAAGCTCACTCCCCAATCCATAACGCTTTCACGCTCCAAGCCCCTCACCGTCTTCGCCGCCACCAAGAAGGCCGTCGCCGTCCTCAAGGGGACCTCCGCCGTCGAAGGCGTCGCCACTCTCATCCAAGAAGACGATGGCCCGACGACAGTTTCTGTTCGCATCACTGGCCTTACTCCGGGGCTTCATGGTTTTCACCTACATGAGTATGGTGATACGACAAATGGGTGTATTTCTACGGGAGCACATTTTAATCCTAATAAATTGACACATGGTGCTCCTGAGGATGAAGTCCGTCATGCGGGTGACCTGGGAAACATAGTTGCTAATGCAGAGGGGGTTGCAGAGGCTACAATTGTGGATAATCAGATACCACTCTCTGGCCCCAATTCAGTAGTTGGAAGAGCCTTGGTGGTCCATGAGCTTGAGGATGACCTTGGAAAGGGTGGGCATGAACTCAGTTTGACAACTGGAAATGCTGGTGGAAGATTAGCATGTGAGGGCGAGCCCTGGTGCAGTGGTAAAGTTGTGCCTTGGTGA

>Glyma11g19840.2   sequence type=CDS   gene model=Glyma11g19840   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGCAGCTAGCAATGGCGGCCAACGCTGTCGTTTCACCGTCGCCGTTCCGACCTCAGCCCTTTCTCCGGTCATCCTTCTCCGGCGTCTCCGTCAAGCTCACTCCCCAATCCATAACGCTTTCACGCTCCAAGCCCCTCACCGTCTTCGCCGCCACCAAGAAGGCCGTCGCCGTCCTCAAGGGGACCTCCGCCGTCGAAGGCGTCGCCACTCTCATCCAAGAAGACGATGGCCCGACGACAGTTTCTGTTCGCATCACTGGCCTTACTCCGGGGCTTCATGGTTTTCACCTACATGAGTATGGTGATACGACAAATGGGTGTATTTCTACGGGAGCACATTTTAATCCTAATAAATTGACACATGGTGCTCCTGAGGATGAAGTCCGTCATGCGGGTGACCTGGGAAACATAGTTGCTAATGCAGAGGGGGTTGCAGAGGCTACAATTGTGGATAATCAGATACCACTCTCTGGCCCCAATTCAGTAGTTGGAAGAGCCTTGGTGGTCCATGAGCTTGAGGATGACCTTGGAAAGGGTGGGCATGAACTCAGTTTGACAACTGGAAATGCTGGTGGAAGATTAGCATGTGGTGTGGTTGGTTTGACTCCAGCATAA

>Glyma11g19840.3   sequence type=CDS   gene model=Glyma11g19840   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGCAGCTAGCAATGGCGGCCAACGCTGTCGTTTCACCGTCGCCGTTCCGACCTCAGCCCTTTCTCCGGTCATCCTTCTCCGGCGTCTCCGTCAAGCTCACTCCCCAATCCATAACGCTTTCACGCTCCAAGCCCCTCACCGTCTTCGCCGCCACCAAGAAGGCCGTCGCCGTCCTCAAGGGGACCTCCGCCGTCGAAGGCGTCGCCACTCTCATCCAAGAAGACGATGGCCCGACGACAGTTTCTGTTCGCATCACTGGCCTTACTCCGGGGCTTCATGGTTTTCACCTACATGAGTATGGTGATACGACAAATGGGTGTATTTCTACGGGAGCACATTTTAATCCTAATAAATTGACACATGGTGCTCCTGAGGATGAAGTCCGTCATGCGGGTGACCTGGGAAACATAGTTGCTAATGCAGAGGGGGTTGCAGAGGCTACAATTGTGGATAATCAGATACCACTCTCTGGCCCCAATTCAGTAGTTGGAAGAGCCTTGGTGGTCCATGAGCTTGAGGATGACCTTGGAAAGGGTGGGCATGAACTCAGTTTGACAACTGGAAATGCTGGTGGAAGATTAGCATGTGTGGTTGGTTTGACTCCAGCATAA

Predicted protein sequences of Glyma11g19840

Limit To All Plant Sequences

>Glyma11g19840.1   sequence type=predicted peptide   gene model=Glyma11g19840   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MQLAMAANAVVSPSPFRPQPFLRSSFSGVSVKLTPQSITLSRSKPLTVFAATKKAVAVLKGTSAVEGVATLIQEDDGPTTVSVRITGLTPGLHGFHLHEYGDTTNGCISTGAHFNPNKLTHGAPEDEVRHAGDLGNIVANAEGVAEATIVDNQIPLSGPNSVVGRALVVHELEDDLGKGGHELSLTTGNAGGRLACEGEPWCSGKVVPW*

>Glyma11g19840.2   sequence type=predicted peptide   gene model=Glyma11g19840   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MQLAMAANAVVSPSPFRPQPFLRSSFSGVSVKLTPQSITLSRSKPLTVFAATKKAVAVLKGTSAVEGVATLIQEDDGPTTVSVRITGLTPGLHGFHLHEYGDTTNGCISTGAHFNPNKLTHGAPEDEVRHAGDLGNIVANAEGVAEATIVDNQIPLSGPNSVVGRALVVHELEDDLGKGGHELSLTTGNAGGRLACGVVGLTPA*

>Glyma11g19840.3   sequence type=predicted peptide   gene model=Glyma11g19840   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MQLAMAANAVVSPSPFRPQPFLRSSFSGVSVKLTPQSITLSRSKPLTVFAATKKAVAVLKGTSAVEGVATLIQEDDGPTTVSVRITGLTPGLHGFHLHEYGDTTNGCISTGAHFNPNKLTHGAPEDEVRHAGDLGNIVANAEGVAEATIVDNQIPLSGPNSVVGRALVVHELEDDLGKGGHELSLTTGNAGGRLACVVGLTPA*

Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA

U.S. Public Domain