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/Glyma02g38540): 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/Glyma02g38540): 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 Glyma02g38540

Feature Type:gene_model
Chromosome:Gm02
Start:43941834
stop:43945041
Source:JGI
Version:Wm82.a1.v1.1
High confidence:yes



A newer version of this gene model can be found here:

Database IDAnnotation TypeAnnotation DescriptionAnnotation SourceMatch ScoreEvidence Code
AT3G13570AT Annotation by Michelle Graham. TAIR10: SC35-like splicing factor 30A | chr3:4429564-4431602 REVERSE LENGTH=262 SoyBaseE_val: 3.00E-73ISS
GO:0000398GO-bp Annotation by Michelle Graham. GO Biological Process: mRNA splicing, via spliceosome SoyBaseN/AISS
GO:0006355GO-bp Annotation by Michelle Graham. GO Biological Process: regulation of transcription, DNA-dependent SoyBaseN/AISS
GO:0008380GO-bp Annotation by Michelle Graham. GO Biological Process: RNA splicing SoyBaseN/AISS
GO:0030422GO-bp Annotation by Michelle Graham. GO Biological Process: production of siRNA involved in RNA interference SoyBaseN/AISS
GO:0035196GO-bp Annotation by Michelle Graham. GO Biological Process: production of miRNAs involved in gene silencing by miRNA SoyBaseN/AISS
GO:0043687GO-bp Annotation by Michelle Graham. GO Biological Process: post-translational protein modification SoyBaseN/AISS
GO:0045893GO-bp Annotation by Michelle Graham. GO Biological Process: positive regulation of transcription, DNA-dependent SoyBaseN/AISS
GO:0005634GO-cc Annotation by Michelle Graham. GO Cellular Compartment: nucleus SoyBaseN/AISS
GO:0005829GO-cc Annotation by Michelle Graham. GO Cellular Compartment: cytosol SoyBaseN/AISS
GO:0016607GO-cc Annotation by Michelle Graham. GO Cellular Compartment: nuclear speck SoyBaseN/AISS
GO:0000166GO-mf Annotation by Michelle Graham. GO Molecular Function: nucleotide binding SoyBaseN/AISS
GO:0003676GO-mf Annotation by Michelle Graham. GO Molecular Function: nucleic acid binding SoyBaseN/AISS
GO:0003723GO-mf Annotation by Michelle Graham. GO Molecular Function: RNA binding SoyBaseN/AISS
KOG0114 KOG Predicted RNA-binding protein (RRM superfamily) JGI ISS
KOG4207 KOG Predicted splicing factor, SR protein superfamily JGI ISS
PTHR23147Panther SERINE/ARGININE RICH SPLICING FACTOR JGI ISS
PF00076PFAM RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) JGI ISS
UniRef100_G7J9M2UniRef Annotation by Michelle Graham. Most informative UniRef hit: Arginine/serine-rich splicing factor n=2 Tax=Medicago truncatula RepID=G7J9M2_MEDTR SoyBaseE_val: 5.00E-92ISS
UniRef100_I1JH68UniRef Annotation by Michelle Graham. Best UniRef hit: Uncharacterized protein n=1 Tax=Glycine max RepID=I1JH68_SOYBN SoyBaseE_val: 1.00E-168ISS

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

Glyma02g38540 not represented in the dataset

Glyma02g38540 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

ParalogEvidenceComments
Glyma14g36670 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.

Corresponding NameAnnotation VersionEvidenceComments
Glyma.02g220800 Wm82.a2.v1IGC As supplied by JGI

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

>Glyma02g38540.2   sequence type=transcript   gene model=Glyma02g38540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
TGCCATCAAAAAATGGTATTTGTATACACGAAACGACGGAGACTAAATCTCTAAAACGCTTGAAACCCTAAAACTCTGTGTCCTCCGCCGTTCACATCATTGTCGACGTTCGTTCAGTTGCTCACACTCTCAACAGAGAAGAGAAGAGAATGAGAGGAAGGAGCTATAGTCCATCGCCTCCTCCTCCACGTTACAGCAGAAGAGGAGGAGGGAGGAGTCCCAGCCCTAGGGGCCGCTATCCTCCCCGTCCCCGACAACAAGATCTCCCTACCAGCCTTCTTGTTCGTAACCTTCGTCATGACTGTAGGCCTGAGGATCTTCGCAGACCTTTTGGTCAATTTGGTCCTCTCAAGGACATTTACCTTCCTAAGGATTACTACACTGGAGAACCCCGTGGCTTTGGTTTTGTCCAATTTGTGGATCCTGCGGATGCTGCTGATGCCAAATATCATATGGATGGTCAAGTTCTTCTTGGTCGGGAGCTCACTGTTGTTTTTGCTGAAGAGAATAGAAAGAAGCCAACTGAGATGAGGACAAGAGAGAGAAGGGGTCGATTTTCTGATCGTAGGAGGTCTCCTCCTCGTTACTCTCGTTCACCTCGCTACTCTCGTTCACCTCGCTACTCTCGGTCTCCACCACCACGTCATAGATCTCGTTCTCACAGTCGTGACTATTATTCTCCTAAACGAAGGGAGTATTCAAGGTATGTGGCCTGTAATAATCGATAACTAAAAATTATTTTTGTTATATGTAATTGTTTTAAACGTCATTACTTTTGATTTGGTTCTTATTTAACACACGAAAGAGCTGGTGTTGTTAAATAGTTGTAATATAG

>Glyma02g38540.1   sequence type=CDS   gene model=Glyma02g38540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGAGAGGAAGGAGCTATAGTCCATCGCCTCCTCCTCCACGTTACAGCAGAAGAGGAGGAGGGAGGAGTCCCAGCCCTAGGGGCCGCTATCCTCCCCGTCCCCGACAACAAGATCTCCCTACCAGCCTTCTTGTTCGTAACCTTCGTCATGACTGTAGGCCTGAGGATCTTCGCAGACCTTTTGGTCAATTTGGTCCTCTCAAGGACATTTACCTTCCTAAGGATTACTACACTGGAGAACCCCGTGGCTTTGGTTTTGTCCAATTTGTGGATCCTGCGGATGCTGCTGATGCCAAATATCATATGGATGGTCAAGTTCTTCTTGGTCGGGAGCTCACTGTTGTTTTTGCTGAAGAGAATAGAAAGAAGCCAACTGAGATGAGGACAAGAGAGAGAAGGGGTCGATTTTCTGATCGTAGGAGGTCTCCTCCTCGTTACTCTCGTTCACCTCGCTACTCTCGTTCACCTCGCTACTCTCGGTCTCCACCACCACGTCATAGATCTCGTTCTCACAGTCGTGACTATTATTCTCCTAAACGAAGGGAGTATTCAAGATCTGTCTCCCCTGAGGGTAGAAGGTACAGTCGAGAAAGATCATATTCACAGCATAATAGAGAGAGGTCATTCTCACGTTCCCCACCTTATAATGGGGGCTCAAGGAGCCGTAGTCAGAGTCCAGCAAAGGGCCCAGGCCGGAGCAGGAGTCCGAGTCTGAATCGAGATGAAAGGGAACCAGCCCGAGGTAGGTCCCCCAGTCAGTGA

>Glyma02g38540.2   sequence type=CDS   gene model=Glyma02g38540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGAGAGGAAGGAGCTATAGTCCATCGCCTCCTCCTCCACGTTACAGCAGAAGAGGAGGAGGGAGGAGTCCCAGCCCTAGGGGCCGCTATCCTCCCCGTCCCCGACAACAAGATCTCCCTACCAGCCTTCTTGTTCGTAACCTTCGTCATGACTGTAGGCCTGAGGATCTTCGCAGACCTTTTGGTCAATTTGGTCCTCTCAAGGACATTTACCTTCCTAAGGATTACTACACTGGAGAACCCCGTGGCTTTGGTTTTGTCCAATTTGTGGATCCTGCGGATGCTGCTGATGCCAAATATCATATGGATGGTCAAGTTCTTCTTGGTCGGGAGCTCACTGTTGTTTTTGCTGAAGAGAATAGAAAGAAGCCAACTGAGATGAGGACAAGAGAGAGAAGGGGTCGATTTTCTGATCGTAGGAGGTCTCCTCCTCGTTACTCTCGTTCACCTCGCTACTCTCGTTCACCTCGCTACTCTCGGTCTCCACCACCACGTCATAGATCTCGTTCTCACAGTCGTGACTATTATTCTCCTAAACGAAGGGAGTATTCAAGGTATGTGGCCTGTAATAATCGATAA

>Glyma02g38540.1   sequence type=predicted peptide   gene model=Glyma02g38540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MRGRSYSPSPPPPRYSRRGGGRSPSPRGRYPPRPRQQDLPTSLLVRNLRHDCRPEDLRRPFGQFGPLKDIYLPKDYYTGEPRGFGFVQFVDPADAADAKYHMDGQVLLGRELTVVFAEENRKKPTEMRTRERRGRFSDRRRSPPRYSRSPRYSRSPRYSRSPPPRHRSRSHSRDYYSPKRREYSRSVSPEGRRYSRERSYSQHNRERSFSRSPPYNGGSRSRSQSPAKGPGRSRSPSLNRDEREPARGRSPSQ*

>Glyma02g38540.2   sequence type=predicted peptide   gene model=Glyma02g38540   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MRGRSYSPSPPPPRYSRRGGGRSPSPRGRYPPRPRQQDLPTSLLVRNLRHDCRPEDLRRPFGQFGPLKDIYLPKDYYTGEPRGFGFVQFVDPADAADAKYHMDGQVLLGRELTVVFAEENRKKPTEMRTRERRGRFSDRRRSPPRYSRSPRYSRSPRYSRSPPPRHRSRSHSRDYYSPKRREYSRYVACNNR*







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