Glyma01g41401 - 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/Glyma01g41401): 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/Glyma01g41401): 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 Glyma01g41401

Feature Type:	gene_model
Chromosome:	Gm01
Start:	52906368
stop:	52908690
Source:	JGI
Version:	Wm82.a1.v1.1
High confidence:	yes

A newer version of this gene model can be found here:

Annotations for Glyma01g41401

Database ID	Annotation Type	Annotation Description	Annotation Source	Match Score	Evidence Code
AT4G17560	AT	Annotation by Michelle Graham. TAIR10: Ribosomal protein L19 family protein \| chr4:9780343-9781752 FORWARD LENGTH=225	SoyBase	E_val: 4.00E-71	ISS
GO:0006412	GO-bp	Annotation by Michelle Graham. GO Biological Process: translation	SoyBase	N/A	ISS
GO:0010267	GO-bp	Annotation by Michelle Graham. GO Biological Process: production of ta-siRNAs involved in RNA interference	SoyBase	N/A	ISS
GO:0019288	GO-bp	Annotation by Michelle Graham. GO Biological Process: isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway	SoyBase	N/A	ISS
GO:0035196	GO-bp	Annotation by Michelle Graham. GO Biological Process: production of miRNAs involved in gene silencing by miRNA	SoyBase	N/A	ISS
GO:0042254	GO-bp	Annotation by Michelle Graham. GO Biological Process: ribosome biogenesis	SoyBase	N/A	ISS
GO:0051607	GO-bp	Annotation by Michelle Graham. GO Biological Process: defense response to virus	SoyBase	N/A	ISS
GO:0005622	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: intracellular	SoyBase	N/A	ISS
GO:0005840	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: ribosome	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:0009941	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: chloroplast envelope	SoyBase	N/A	ISS
GO:0016020	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: membrane	SoyBase	N/A	ISS
GO:0003735	GO-mf	Annotation by Michelle Graham. GO Molecular Function: structural constituent of ribosome	SoyBase	N/A	ISS
PTHR15680	Panther	50S RIBOSOMAL PROTEIN L19	JGI		ISS
PTHR15680:SF2	Panther	50S RIBOSOMAL PROTEIN L19	JGI		ISS
PF01245	PFAM	Ribosomal protein L19	JGI		ISS
UniRef100_B7FKU8	UniRef	Annotation by Michelle Graham. Most informative UniRef hit: 50S ribosomal protein L19 n=1 Tax=Medicago truncatula RepID=B7FKU8_MEDTR	SoyBase	E_val: 8.00E-96	ISS
UniRef100_I1J9R5	UniRef	Annotation by Michelle Graham. Best UniRef hit: Uncharacterized protein n=2 Tax=Glycine max RepID=I1J9R5_SOYBN	SoyBase	E_val: 2.00E-150	ISS

Expression Patterns of Glyma01g41401

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

Glyma01g41401 not represented in the dataset	Glyma01g41401 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 Glyma01g41401

Paralog	Evidence	Comments
Glyma11g04020	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 Glyma01g41401 Gene Call Version Wm82.a1.v1.1

Corresponding Name	Annotation Version	Evidence	Comments
Glyma.01g205400	Wm82.a2.v1	IGC	As supplied by JGI

References for Glyma01g41401

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

Transcripts of Glyma01g41401

Limit To All Plant Sequences

>Glyma01g41401.2   sequence type=transcript   gene model=Glyma01g41401   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
GGAACATGATGGGCTGAATAGGGCCTTACATTTTTTCCGGCCAGGCCCAAGCCAGATAAAGGAAAAAAGAAGAGTTGTAGTTGACACGTGTGGAACGGATAGAGAAACAGATAAGGGCGCTCTCCGTACCATCTTCCTAATCCTCCTTACATTTGCAGTGTTCCCATGTCTCCTACCCACTGAAGTCGAACCCCTATTTTTCCTCTCCCTAATGGCTTCTCAAGTTCTTCTTCAGGCACTGTTTGCCCCCAAGCTAAGTTTCCCTTCTTCTTCTCGTAACGTGGCGTTAATTTCTAGGGTTCCTTCCACCCCAATTTCATGGCGTTGCACTCCCCTCATTGCTAAGCCTAGTTTCGTAGTGAGAGCTGACACCAACCTCGATGGCGGTGGTGAAGCCACCGAGGATGTTCCTTCGGATAATGCTGAAAAAGTTTCGGAAGGCGAAGCAGAACAAGTTTCGGATTCTGAAGCTCCGAAATCGCCTAGAAAACCCCGAGTCAAACTCGGAGACATTATGGGGATATTGAATCAGAGGGCAATTGAGGCATCCGAGAAGCAAAGACCAACTCCAGACATTAGGACTGGGGATATTGTCGAAATCAAATTGGAGGTTCCTGAGAACAAGCGTAGGTTGTCCATTTATAAAGGGATTGTCATCTCAAAACAAAATGCTGGTATTCACACGACTATTCGAATCCGAAGAATCATTGCCGGCACTGGGGTTGAGATAGTCTTCCCAGTTTACTCACCAAACATCAAAGAAATCAAAGTGGTAAGTCACCGTAAGGTCAGGAGGGCAAGATTGTACTATCTGAGAGACAAGCTTCCGAGATTCTCCACTTTCAAGTGATACTCGGATACCCCACCTTTCCTCACGTTATTCGTCGAACTAGTCTGCTGATCCAGGATAAGTGCTGCGGAGCTTTAATTTTTTTAATTTCAATTTGTTCTGTTGTAGAATACATCATTTTTCTTCCCCTTTGTGTATCTTCCCTTAAATCGAAACAAGTGTACTGAACCTTGATAGTATTGAGAAATTTGAAGTGTTTCTTCTGCATCACCATATATAGTTTATTCGGTAGAAATCGAAGCTATGAAGAAAATATTATTTTAGTATTAAAATGTAGGATTATAACAGTAAAGGTTTAAAATCTAGAATCATA

Coding sequences of Glyma01g41401

Limit To All Plant Sequences

>Glyma01g41401.1   sequence type=CDS   gene model=Glyma01g41401   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGGCTTCTCAAGTTCTTCTTCAGCAGGCACTGTTTGCCCCCAAGCTAAGTTTCCCTTCTTCTTCTCGTAACGTGGCGTTAATTTCTAGGGTTCCTTCCACCCCAATTTCATGGCGTTGCACTCCCCTCATTGCTAAGCCTAGTTTCGTAGTGAGAGCTGACACCAACCTCGATGGCGGTGGTGAAGCCACCGAGGATGTTCCTTCGGATAATGCTGAAAAAGTTTCGGAAGGCGAAGCAGAACAAGTTTCGGATTCTGAAGCTCCGAAATCGCCTAGAAAACCCCGAGTCAAACTCGGAGACATTATGGGGATATTGAATCAGAGGGCAATTGAGGCATCCGAGAAGCAAAGACCAACTCCAGACATTAGGACTGGGGATATTGTCGAAATCAAATTGGAGGTTCCTGAGAACAAGCGTAGGTTGTCCATTTATAAAGGGATTGTCATCTCAAAACAAAATGCTGGTATTCACACGACTATTCGAATCCGAAGAATCATTGCCGGCACTGGGGTTGAGATAGTCTTCCCAGTTTACTCACCAAACATCAAAGAAATCAAAGTGGTAAGTCACCGTAAGGTCAGGAGGGCAAGATTGTACTATCTGAGAGACAAGCTTCCGAGATTCTCCACTTTCAAGTGA

>Glyma01g41401.2   sequence type=CDS   gene model=Glyma01g41401   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGGCTTCTCAAGTTCTTCTTCAGGCACTGTTTGCCCCCAAGCTAAGTTTCCCTTCTTCTTCTCGTAACGTGGCGTTAATTTCTAGGGTTCCTTCCACCCCAATTTCATGGCGTTGCACTCCCCTCATTGCTAAGCCTAGTTTCGTAGTGAGAGCTGACACCAACCTCGATGGCGGTGGTGAAGCCACCGAGGATGTTCCTTCGGATAATGCTGAAAAAGTTTCGGAAGGCGAAGCAGAACAAGTTTCGGATTCTGAAGCTCCGAAATCGCCTAGAAAACCCCGAGTCAAACTCGGAGACATTATGGGGATATTGAATCAGAGGGCAATTGAGGCATCCGAGAAGCAAAGACCAACTCCAGACATTAGGACTGGGGATATTGTCGAAATCAAATTGGAGGTTCCTGAGAACAAGCGTAGGTTGTCCATTTATAAAGGGATTGTCATCTCAAAACAAAATGCTGGTATTCACACGACTATTCGAATCCGAAGAATCATTGCCGGCACTGGGGTTGAGATAGTCTTCCCAGTTTACTCACCAAACATCAAAGAAATCAAAGTGGTAAGTCACCGTAAGGTCAGGAGGGCAAGATTGTACTATCTGAGAGACAAGCTTCCGAGATTCTCCACTTTCAAGTGA

Predicted protein sequences of Glyma01g41401

Limit To All Plant Sequences

>Glyma01g41401.1   sequence type=predicted peptide   gene model=Glyma01g41401   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MASQVLLQQALFAPKLSFPSSSRNVALISRVPSTPISWRCTPLIAKPSFVVRADTNLDGGGEATEDVPSDNAEKVSEGEAEQVSDSEAPKSPRKPRVKLGDIMGILNQRAIEASEKQRPTPDIRTGDIVEIKLEVPENKRRLSIYKGIVISKQNAGIHTTIRIRRIIAGTGVEIVFPVYSPNIKEIKVVSHRKVRRARLYYLRDKLPRFSTFK*

>Glyma01g41401.2   sequence type=predicted peptide   gene model=Glyma01g41401   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MASQVLLQALFAPKLSFPSSSRNVALISRVPSTPISWRCTPLIAKPSFVVRADTNLDGGGEATEDVPSDNAEKVSEGEAEQVSDSEAPKSPRKPRVKLGDIMGILNQRAIEASEKQRPTPDIRTGDIVEIKLEVPENKRRLSIYKGIVISKQNAGIHTTIRIRRIIAGTGVEIVFPVYSPNIKEIKVVSHRKVRRARLYYLRDKLPRFSTFK*

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