Glyma16g04000 - SoyBase

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

Report for Sequence Feature Glyma16g04000

Feature Type:	gene_model
Chromosome:	Gm16
Start:	3357900
stop:	3360632
Source:	JGI
Version:	Wm82.a1.v1.1
High confidence:	yes

A newer version of this gene model can be found here:

Annotations for Glyma16g04000

Database ID	Annotation Type	Annotation Description	Annotation Source	Match Score	Evidence Code
AT3G03700	AT	Annotation by Michelle Graham. TAIR10: Plasma-membrane choline transporter family protein \| chr3:916503-918327 FORWARD LENGTH=482	SoyBase	E_val: 7.00E-155	ISS
GO:0008150	GO-bp	Annotation by Michelle Graham. GO Biological Process: biological process	SoyBase	N/A	ISS
GO:0005886	GO-cc	Annotation by Michelle Graham. GO Cellular Compartment: plasma membrane	SoyBase	N/A	ISS
KOG1362	KOG	Choline transporter-like protein	JGI		ISS
PTHR12385	Panther	CTL TRANSPORTER	JGI		ISS
PTHR12385:SF1	Panther	CTL1	JGI		ISS
PF04515	PFAM	Plasma-membrane choline transporter	JGI		ISS
UniRef100_G7L1K3	UniRef	Annotation by Michelle Graham. Most informative UniRef hit: Protein pns1 n=1 Tax=Medicago truncatula RepID=G7L1K3_MEDTR	SoyBase	E_val: 0	ISS
UniRef100_I1MKW0	UniRef	Annotation by Michelle Graham. Best UniRef hit: Uncharacterized protein n=2 Tax=Glycine max RepID=I1MKW0_SOYBN	SoyBase	E_val: 0	ISS

Expression Patterns of Glyma16g04000

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 Glyma16g04000

Paralog	Evidence	Comments
Glyma19g29550	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 Glyma16g04000 Gene Call Version Wm82.a1.v1.1

Corresponding Name	Annotation Version	Evidence	Comments
Glyma.16g035700	Wm82.a2.v1	IGC	As supplied by JGI

References for Glyma16g04000

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

Transcripts of Glyma16g04000

Limit To All Plant Sequences

>Glyma16g04000.2   sequence type=transcript   gene model=Glyma16g04000   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
TGAACATGCTGCACTAAAAAGAAAGAAGAAAAAAAATGAATTGAGAGAAAAACGAGGACTGAGTCAGTTGCTTGTGTAGCAAGTGTGGTGTGAAATTGTGAATATTGACTTCGATTAGAGAGCAACAAGACTTGAGTAATATTAATATTGTATGGTTTCTTAGACAAGATTTGAAGAGTTTTCCATCTGGGCCAAGAAAGTGAAAGAAAATCATAAGAAACTCTTTGTGAGGAGATTGAAAATTGTGAATGCATCTCAAATAGATCAATAGCATAGTCATTGGCCATGTTGAACAACTCTGATACCACCACACCACCTCCACAGATCATCCAAATCCCACCACAAGTTCCACAGCAAAGGCTTTCATTCTCGGTCCCCATCAAGGCACAAGTTTCAAGCTTTCCTAACACAACAACAGTGGCGGCTCAAACAGCAAGAAGGGTCTTCAAGATTCTCTTCTACTTGCATTTGTTCCTAGTTGCAGCCTTGGTGACTTTCCTTACCATATATGGTCTTGTCTCTGATTCTCACACCCACCATTTCCACCCCAAGAAATGGTACCCTCCACTTCTTGCATCAACAGCATGTGCTGGAATTGTTGGTTTCACATGGCAATGGATCACTGCAAGCCACTCCACAAGGGTGGTTAGGTTGGTATTTTGGCTTAGTCCCCTTCTAACATGTGCAATGGGAATTATGTTTGTGTGCATTGGCACTGCAGTGAGTCTGGCAGTTGGTGTAATTGCTTTGGTTTGTGCATTAGTTCAATCCCTCTATTTTTGTTGGGTCAATCCTAGATTTGAATATGCCACAAAAATCTTGTCAGTTTCAGTAGCTTTTCCTCCAAACAGAACCCAGGGGCTAACCCTTTATTCAATCCTCATTGGAATCCTTTATTGCTGTTTTCTGTTGGCTGGGATTGGAGGGGCTAGAGCAATTGAAAACAGAACCCAACTAGCAGAATTTTTCATCTTCTTGATCTTGCTGAGCCTAGGGTGGACTATGCAGTTTCTGAAGAATGCAATGTATGTCACTATTTCAAGGGTCAAGTACATGCATTTTGCAGGAGGAGTTGACATGGACACTAGAGTGGCAGTTTGTGACACAATCAAGCACTTAACTGGAAGTGTTTCCATGGGCTCCATCCTCGTTCCCGTCATTGTGCTCTTCCGGGGTTTTGCACGAACCACGAGTCTGGTTGGAGGAGACACAGATGAATTCATGTTTTCCTGTGTTAGCTGCTATATGGGGGTAGCATCTCTTCTTGTGGTCCGTGGGAACCGGTGGGGTTTTGTGCATGTTGGAGTTTATAACAAAGGGTTTGTGCAGGCATCTTGTGATACTTGGGAGATGTTCATTAGAGTTGGATTGGAGCAACTCATAGACTTGGATCTCACAGGGGCATTCTGTTTCCTTAGTGGTGTTGGAACAGGTGCAATATGTAGTCTGGTGAGTGGAATTTGGAGTATTGTAATGCACAAGAGCTATGCCACAGAAGTGTCCATTTATGCTTTCCTCATTGGATATTTCATGTGTCGATTGGCTATTGCATGGGTACAAGCTTGTGTTTCAGCTTACTATGTTGCCTACGCAGAAAATCCACAGAGCACTCAGTTTGATTCCACTATTCCAATACGCTTGGAGCAGCTTAATAGATCTCAAGCTTTGCAAATATTCAGAGCTAATAATTTGAGCTGAGTCTAAATAATGAAGGAACAGTAATTCAAGTTAACTTCATTATCCCCTGGGATTTGGAAGGACAATTTTTGCATTGTATATAATGATTTAGTTTTTGATGTAGTCTTGAATTATGTTAAATCTTTATAATGCCGGTTCTCTATTTTTGTACATGAATATAGACAGCAACATGCAATGAACAGCTCCATTTAGTTAGGACTGATAGTCATAGCTGATAGTGTACAACTGAAACAACAAAACCATATGTTATATATATATATATATATAAACCATGACCACAAGATTAATAG

Coding sequences of Glyma16g04000

Limit To All Plant Sequences

>Glyma16g04000.1   sequence type=CDS   gene model=Glyma16g04000   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGGGAATTATGTTTGTGTGCATTGGCACTGCAGTGAGTCTGGCAGTTGGTGTAATTGCTTTGGTTTGTGCATTAGTTCAATCCCTCTATTTTTGTTGGGTCAATCCTAGATTTGAATATGCCACAAAAATCTTGTCAGTTTCAGTAGCTTTTCCTCCAAACAGAACCCAGGGGCTAACCCTTTATTCAATCCTCATTGGAATCCTTTATTGCTGTTTTCTGTTGGCTGGGATTGGAGGGGCTAGAGCAATTGAAAACAGAACCCAACTAGCAGAATTTTTCATCTTCTTGATCTTGCTGAGCCTAGGGTGGACTATGCAGTTTCTGAAGAATGCAATGTATGTCACTATTTCAAGGGTCAAGTACATGCATTTTGCAGGAGGAGTTGACATGGACACTAGAGTGGCAGTTTGTGACACAATCAAGCACTTAACTGGAAGTGTTTCCATGGGCTCCATCCTCGTTCCCGTCATTGTGCTCTTCCGGGGTTTTGCACGAACCACGAGTCTGGTTGGAGGAGACACAGATGAATTCATGTTTTCCTGTGTTAGCTGCTATATGGGGGTAGCATCTCTTCTTGTGGTCCGTGGGAACCGGTGGGGTTTTGTGCATGTTGGAGTTTATAACAAAGGGTTTGTGCAGGCATCTTGTGATACTTGGGAGATGTTCATTAGAGTTGGATTGGAGCAACTCATAGACTTGGATCTCACAGGGGCATTCTGTTTCCTTAGTGGTGTTGGAACAGGTGCAATATGTAGTCTGGTGAGTGGAATTTGGAGTATTGTAATGCACAAGAGCTATGCCACAGAAGTGTCCATTTATGCTTTCCTCATTGGATATTTCATGTGTCGATTGGCTATTGCATGGGTACAAGCTTGTGTTTCAGCTTACTATGTTGCCTACGCAGAAAATCCACAGAGCACTCAGTTTGATTCCACTATTCCAATACGCTTGGAGCAGCTTAATAGATCTCAAGCTTTGCAAATATTCAGAGCTAATAATTTGAGCTGA

>Glyma16g04000.2   sequence type=CDS   gene model=Glyma16g04000   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
ATGTTGAACAACTCTGATACCACCACACCACCTCCACAGATCATCCAAATCCCACCACAAGTTCCACAGCAAAGGCTTTCATTCTCGGTCCCCATCAAGGCACAAGTTTCAAGCTTTCCTAACACAACAACAGTGGCGGCTCAAACAGCAAGAAGGGTCTTCAAGATTCTCTTCTACTTGCATTTGTTCCTAGTTGCAGCCTTGGTGACTTTCCTTACCATATATGGTCTTGTCTCTGATTCTCACACCCACCATTTCCACCCCAAGAAATGGTACCCTCCACTTCTTGCATCAACAGCATGTGCTGGAATTGTTGGTTTCACATGGCAATGGATCACTGCAAGCCACTCCACAAGGGTGGTTAGGTTGGTATTTTGGCTTAGTCCCCTTCTAACATGTGCAATGGGAATTATGTTTGTGTGCATTGGCACTGCAGTGAGTCTGGCAGTTGGTGTAATTGCTTTGGTTTGTGCATTAGTTCAATCCCTCTATTTTTGTTGGGTCAATCCTAGATTTGAATATGCCACAAAAATCTTGTCAGTTTCAGTAGCTTTTCCTCCAAACAGAACCCAGGGGCTAACCCTTTATTCAATCCTCATTGGAATCCTTTATTGCTGTTTTCTGTTGGCTGGGATTGGAGGGGCTAGAGCAATTGAAAACAGAACCCAACTAGCAGAATTTTTCATCTTCTTGATCTTGCTGAGCCTAGGGTGGACTATGCAGTTTCTGAAGAATGCAATGTATGTCACTATTTCAAGGGTCAAGTACATGCATTTTGCAGGAGGAGTTGACATGGACACTAGAGTGGCAGTTTGTGACACAATCAAGCACTTAACTGGAAGTGTTTCCATGGGCTCCATCCTCGTTCCCGTCATTGTGCTCTTCCGGGGTTTTGCACGAACCACGAGTCTGGTTGGAGGAGACACAGATGAATTCATGTTTTCCTGTGTTAGCTGCTATATGGGGGTAGCATCTCTTCTTGTGGTCCGTGGGAACCGGTGGGGTTTTGTGCATGTTGGAGTTTATAACAAAGGGTTTGTGCAGGCATCTTGTGATACTTGGGAGATGTTCATTAGAGTTGGATTGGAGCAACTCATAGACTTGGATCTCACAGGGGCATTCTGTTTCCTTAGTGGTGTTGGAACAGGTGCAATATGTAGTCTGGTGAGTGGAATTTGGAGTATTGTAATGCACAAGAGCTATGCCACAGAAGTGTCCATTTATGCTTTCCTCATTGGATATTTCATGTGTCGATTGGCTATTGCATGGGTACAAGCTTGTGTTTCAGCTTACTATGTTGCCTACGCAGAAAATCCACAGAGCACTCAGTTTGATTCCACTATTCCAATACGCTTGGAGCAGCTTAATAGATCTCAAGCTTTGCAAATATTCAGAGCTAATAATTTGAGCTGA

Predicted protein sequences of Glyma16g04000

Limit To All Plant Sequences

>Glyma16g04000.1   sequence type=predicted peptide   gene model=Glyma16g04000   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MGIMFVCIGTAVSLAVGVIALVCALVQSLYFCWVNPRFEYATKILSVSVAFPPNRTQGLTLYSILIGILYCCFLLAGIGGARAIENRTQLAEFFIFLILLSLGWTMQFLKNAMYVTISRVKYMHFAGGVDMDTRVAVCDTIKHLTGSVSMGSILVPVIVLFRGFARTTSLVGGDTDEFMFSCVSCYMGVASLLVVRGNRWGFVHVGVYNKGFVQASCDTWEMFIRVGLEQLIDLDLTGAFCFLSGVGTGAICSLVSGIWSIVMHKSYATEVSIYAFLIGYFMCRLAIAWVQACVSAYYVAYAENPQSTQFDSTIPIRLEQLNRSQALQIFRANNLS*

>Glyma16g04000.2   sequence type=predicted peptide   gene model=Glyma16g04000   sequence assembly version=Glyma 1.0   annotation version=1.1   JGI Gene Call confidence=high
MLNNSDTTTPPPQIIQIPPQVPQQRLSFSVPIKAQVSSFPNTTTVAAQTARRVFKILFYLHLFLVAALVTFLTIYGLVSDSHTHHFHPKKWYPPLLASTACAGIVGFTWQWITASHSTRVVRLVFWLSPLLTCAMGIMFVCIGTAVSLAVGVIALVCALVQSLYFCWVNPRFEYATKILSVSVAFPPNRTQGLTLYSILIGILYCCFLLAGIGGARAIENRTQLAEFFIFLILLSLGWTMQFLKNAMYVTISRVKYMHFAGGVDMDTRVAVCDTIKHLTGSVSMGSILVPVIVLFRGFARTTSLVGGDTDEFMFSCVSCYMGVASLLVVRGNRWGFVHVGVYNKGFVQASCDTWEMFIRVGLEQLIDLDLTGAFCFLSGVGTGAICSLVSGIWSIVMHKSYATEVSIYAFLIGYFMCRLAIAWVQACVSAYYVAYAENPQSTQFDSTIPIRLEQLNRSQALQIFRANNLS*

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