Oryza sativa Japonica Group SSR "RM184"

Details

Marker Created:
Marker Updated:
Internal Marker Accession:	RM184
Repeat Motif	(CA)7
Anneal Temperature	55
Expected PCR Product Size	219
Sequence Source	U40708
Linkage Group
Remarks

Database Cross-References (2)

Gramene Literature	Temnykh-S, Park-W-D, Ayres-N-M, Cartinhour-S, Hauck-N, Lipovich-L, Cho-Y-G, Ishii-T, McCouch-S-R, "Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.)", Theoretical and applied genetics, 2000, vol. 100, pp. 697-712
Gramene Diversity Rice Marker	146

Sequences (4)

Repeat motif: (CA)7 highlighted on FASTA sequence in red (if found).

Related Sequences (4)

>RM184_forward Oryza sativa Japonica Group Primer [22 bp]. Associated to 'RM184' via primer_forward

 
          atcccattcgccaaaaccggcc

>RM184_reverse Oryza sativa Japonica Group Primer [22 bp]. Associated to 'RM184' via primer_reverse

 
          tgacacttggagagcggtgtgg

>U40708 Oryza sativa Genomic DNA [3250 bp]. Associated to 'RM184' via contained_in_sequence

 
          GTCGACGCTGACTTTCTTTGCCTCTTCTTATCTGCAAATTAAAACCGTTAGTCATGATCATTTTTTAGCTATTTTTATTT
TCGTATTAAAATGAAAATTCCTTACACTCCTAAGCTTTCTTTCTTTCTTTATAAAGGCAATACAAATGCAAGTGCTTATA
TAAAAATGCGTGTATACTTACCCGTATGAACACGCACACACACCCTACTTTATGAGTACTTTCGAATACGGAACCGGCTT
ATCTTGAGATTAACCTATTGCCTACCACTGAAAAAAAAAACTAGGCATAAAATGCTAACATCCATATATACTAATTAAGT
CTAGGACTTTTAGCCAAGTTGAAAAGTTCCACCATCAGAAACCTGACTAGTTACCATTAGGGTTTGAAGTTTCAGAATTT
GTTTTCTTGCCGATGGGGACCGGTAATTTCATAATTTTTTTTGGCTGAAATTATTTGAAAATTTGACTGATTTTGAATGA
ATTTGAATAAAATTTAACCAAATTCACAAAAAATTACAAAAAAAGAAGAAAATTCCGGGTGAGATGTGAGCTTGCCGGTG
GGGTTCGAAATTTCGGAAATTTCGGAAATTTCGAACCGAAATTTCAAACCCTAGTTATGATACGCTCACTTCGTGACTCT
CTTGTGTTCATTTTATTTATGTTCCCCGAAATGACTATATTACCCTTCTCTCGTATTTATACATTGTGAAAATTTCATAC
TTTATTATAAAATCAAACAGGATAGATATATTAGGTCCTTATAATAAAATCAAATAGGATACAAATTCATAAATGTTAGT
GTTTTTTTATAAACTTAAAGTTAAAGAATTTTGACTTAAGAAAAAACTAAAACACTAAAACAACTTACGATACGGAACAA
AGGGAACAATAATTGTTGTTCTAGATACAGATATTTGGGTGGCATGCTTAAAATAAATTTCAGTAATTACGCCCCCCTTT
TGAATGGGCAATTTGTGAACTTCATGAAAAAAGGCGGGTACCTTAGGAGCATAAGTACTGAATTTTATATTCTAATTGAT
CAAATGAATATCCCCTCGTTTATTACTTGACATTCAAATGATTATAAAAAAAATAATATGATAGATTAATCTATATATGA
TATATCATTTCACAAACATGTAACTAAATAACAAATTAAACTAACTATTATGCATACTCATATTTATATTTGTTTTTTTT
ATAATTTATAGAAGTTAAATTTGGTGTTGAATGTTAATTTCTAGAGTGATATATCATATAATAATCTATTTCATTAATTT
TATTTATTTTTTCTAATTATTTGAATGACATGTAAAAAATAAAAGAACATTCCCTCAAGGGATTAGATAGTTTGCTGGTT
CAATGATGCATTTTTATTTGACTAGTATATATATTATTCCCTCCGTTTCATAATGTAAGACTTTCTAGCATTGCTCATAT
TTATATAGATGTTAATGAATCTAGATGCATATATATGTCTAGATTTATTAATATCTGTATGAATATGGGTAATATGCTAA
AAAGACTTGCATTATGAAACGGAGGAAGTATGTCGCCAGGCTCACTTAACATGTTGGTCTAGATCGGTTTAAAATGCTGC
ATTTAAGTCGGAATCAGATCATGTATACATGTAACACAATACTGGTAAGCAGTAAGAAATGCCCGATCTAGGGATGAAAA
AGAATAACTGAGATAATAACTTACCATGCAATTTTATTATTGCACAAATTTAATTAACTGTTTAGTTTGATACTTGGCCT
CATATATAGTACGTAGTAATTAATTAAACCATCGATCTCACTAGGCTCCAACTAGAAATCAGATCCACGTCTACTAGTAC
AGATATGTGATGAGCAGATATAAGTGCATCTGCCACACATCACTGAACCAGCACATGGATCACATTAAGCACGTCAATGT
ATGCTAATTAATTGATTAACTATACCATGCCTAATTGCTTAATTAGCAGCCAACGGTATTCGATTGATCCCATTCGCCAA
AACCGGCCGGAGTCGCTCTCATGAAAACAGCCTCAGATGACCTTGAAGTATGGACAGAATACAATAGCAAACCGATCGAA
TAATTCTATCTCTGCTTACATAAAAGCAAAAGCAAAAGTAAACACACACACACACAAAGCAAAAACAATAAATCAGTATT
CTAAAAATAAATCAGTAACATCACCACACCGCTCTCCAAGTGTCAAAAAGAATTAAAGGACAACAGCTACTGGCACTCTC
CATGAACTCTCCTGGTCATCATTTCACACCCATATACTGTGTCCAAAGTCCAAAAGCTCTAACGTCTCTAGTTTTGGACC
ATGCAGACTGATGAACATCTGATGAGATAGCCATACACGAGATGCACCCTATAAATACCCCAGCTCCCCTTCACTCCAAC
CACACTACCCAGCTCACTGAAGTAGCAACGCAGCTCATCAGTGTCAAGATGGCTACTACTAAGCATTTGGCTCTTGCCAT
CCTTGTCCTCCTTAGCATTGGTATGACCACCAGTGCAAGAACCCTCCTAGGTTATGGCCCCGGAGGTGGAGGTGGTGGTG
GTGGTGAAGGAGGCGGTGGTGGTTACGGTGGATCGGGCTATGGTTCTGGTTCTGGGTATGGTGAGGGAGGTGGTAGTGGA
GGTGCTGCCGGTGGCGGGTATGGGCGTGGTGGAGGCGGCGGCGGCGGTGGTGGTGAGGGTGGTGGCTCCGGCTCTGGCTA
TGGGTCTGGGCAAGGCTCTGGCTATGGTGCAGGTGTTGGTGGTGCTGGCGGGTATGGTAGTGGTGGCGGAGGTGGTGGTG
GCCAAGGTGGTGGTGCTGGCGGCTACGGGCAAGGGTCTGGCTATGGTTCCGGCTATGGGTCGGGTGCTGGTGGTGCTCAT
GGTGGTGGTTATGGAAGTGGTGGCGGTGGCGGTGGCGGTGGAGGCCAAGGTGGAGGCTCCGGCTATGGCTCAGGCTCTGG
ATATGGCTCAGGCTACGGCGGAGGCAACGGACACCACTAAGCTCGTTTACTCTACCAGCTACAATAGCCTGTTGTTATAA
ATGAACCGTGATCAGTAATGAGCCTCTCTCTCTGCTTTACAAAGAGCTTGTCGGATTGTATCGATATAGCACTGTACTGG
TCGGCTTGCCGTTTGATCACATAAGTTGGCAAAGCCTAGTAATTAAATAAAACGATCTTTGTACTAAGATCATACGACTG
TATGACTGAGCTGTTCACTAATATTGATATGCAAGCACATATATTTAACA

>U40708 Oryza sativa Genomic DNA [3250 bp]. Associated to 'RM184' via source_sequence

 
          GTCGACGCTGACTTTCTTTGCCTCTTCTTATCTGCAAATTAAAACCGTTAGTCATGATCATTTTTTAGCTATTTTTATTT
TCGTATTAAAATGAAAATTCCTTACACTCCTAAGCTTTCTTTCTTTCTTTATAAAGGCAATACAAATGCAAGTGCTTATA
TAAAAATGCGTGTATACTTACCCGTATGAACACGCACACACACCCTACTTTATGAGTACTTTCGAATACGGAACCGGCTT
ATCTTGAGATTAACCTATTGCCTACCACTGAAAAAAAAAACTAGGCATAAAATGCTAACATCCATATATACTAATTAAGT
CTAGGACTTTTAGCCAAGTTGAAAAGTTCCACCATCAGAAACCTGACTAGTTACCATTAGGGTTTGAAGTTTCAGAATTT
GTTTTCTTGCCGATGGGGACCGGTAATTTCATAATTTTTTTTGGCTGAAATTATTTGAAAATTTGACTGATTTTGAATGA
ATTTGAATAAAATTTAACCAAATTCACAAAAAATTACAAAAAAAGAAGAAAATTCCGGGTGAGATGTGAGCTTGCCGGTG
GGGTTCGAAATTTCGGAAATTTCGGAAATTTCGAACCGAAATTTCAAACCCTAGTTATGATACGCTCACTTCGTGACTCT
CTTGTGTTCATTTTATTTATGTTCCCCGAAATGACTATATTACCCTTCTCTCGTATTTATACATTGTGAAAATTTCATAC
TTTATTATAAAATCAAACAGGATAGATATATTAGGTCCTTATAATAAAATCAAATAGGATACAAATTCATAAATGTTAGT
GTTTTTTTATAAACTTAAAGTTAAAGAATTTTGACTTAAGAAAAAACTAAAACACTAAAACAACTTACGATACGGAACAA
AGGGAACAATAATTGTTGTTCTAGATACAGATATTTGGGTGGCATGCTTAAAATAAATTTCAGTAATTACGCCCCCCTTT
TGAATGGGCAATTTGTGAACTTCATGAAAAAAGGCGGGTACCTTAGGAGCATAAGTACTGAATTTTATATTCTAATTGAT
CAAATGAATATCCCCTCGTTTATTACTTGACATTCAAATGATTATAAAAAAAATAATATGATAGATTAATCTATATATGA
TATATCATTTCACAAACATGTAACTAAATAACAAATTAAACTAACTATTATGCATACTCATATTTATATTTGTTTTTTTT
ATAATTTATAGAAGTTAAATTTGGTGTTGAATGTTAATTTCTAGAGTGATATATCATATAATAATCTATTTCATTAATTT
TATTTATTTTTTCTAATTATTTGAATGACATGTAAAAAATAAAAGAACATTCCCTCAAGGGATTAGATAGTTTGCTGGTT
CAATGATGCATTTTTATTTGACTAGTATATATATTATTCCCTCCGTTTCATAATGTAAGACTTTCTAGCATTGCTCATAT
TTATATAGATGTTAATGAATCTAGATGCATATATATGTCTAGATTTATTAATATCTGTATGAATATGGGTAATATGCTAA
AAAGACTTGCATTATGAAACGGAGGAAGTATGTCGCCAGGCTCACTTAACATGTTGGTCTAGATCGGTTTAAAATGCTGC
ATTTAAGTCGGAATCAGATCATGTATACATGTAACACAATACTGGTAAGCAGTAAGAAATGCCCGATCTAGGGATGAAAA
AGAATAACTGAGATAATAACTTACCATGCAATTTTATTATTGCACAAATTTAATTAACTGTTTAGTTTGATACTTGGCCT
CATATATAGTACGTAGTAATTAATTAAACCATCGATCTCACTAGGCTCCAACTAGAAATCAGATCCACGTCTACTAGTAC
AGATATGTGATGAGCAGATATAAGTGCATCTGCCACACATCACTGAACCAGCACATGGATCACATTAAGCACGTCAATGT
ATGCTAATTAATTGATTAACTATACCATGCCTAATTGCTTAATTAGCAGCCAACGGTATTCGATTGATCCCATTCGCCAA
AACCGGCCGGAGTCGCTCTCATGAAAACAGCCTCAGATGACCTTGAAGTATGGACAGAATACAATAGCAAACCGATCGAA
TAATTCTATCTCTGCTTACATAAAAGCAAAAGCAAAAGTAAACACACACACACACAAAGCAAAAACAATAAATCAGTATT
CTAAAAATAAATCAGTAACATCACCACACCGCTCTCCAAGTGTCAAAAAGAATTAAAGGACAACAGCTACTGGCACTCTC
CATGAACTCTCCTGGTCATCATTTCACACCCATATACTGTGTCCAAAGTCCAAAAGCTCTAACGTCTCTAGTTTTGGACC
ATGCAGACTGATGAACATCTGATGAGATAGCCATACACGAGATGCACCCTATAAATACCCCAGCTCCCCTTCACTCCAAC
CACACTACCCAGCTCACTGAAGTAGCAACGCAGCTCATCAGTGTCAAGATGGCTACTACTAAGCATTTGGCTCTTGCCAT
CCTTGTCCTCCTTAGCATTGGTATGACCACCAGTGCAAGAACCCTCCTAGGTTATGGCCCCGGAGGTGGAGGTGGTGGTG
GTGGTGAAGGAGGCGGTGGTGGTTACGGTGGATCGGGCTATGGTTCTGGTTCTGGGTATGGTGAGGGAGGTGGTAGTGGA
GGTGCTGCCGGTGGCGGGTATGGGCGTGGTGGAGGCGGCGGCGGCGGTGGTGGTGAGGGTGGTGGCTCCGGCTCTGGCTA
TGGGTCTGGGCAAGGCTCTGGCTATGGTGCAGGTGTTGGTGGTGCTGGCGGGTATGGTAGTGGTGGCGGAGGTGGTGGTG
GCCAAGGTGGTGGTGCTGGCGGCTACGGGCAAGGGTCTGGCTATGGTTCCGGCTATGGGTCGGGTGCTGGTGGTGCTCAT
GGTGGTGGTTATGGAAGTGGTGGCGGTGGCGGTGGCGGTGGAGGCCAAGGTGGAGGCTCCGGCTATGGCTCAGGCTCTGG
ATATGGCTCAGGCTACGGCGGAGGCAACGGACACCACTAAGCTCGTTTACTCTACCAGCTACAATAGCCTGTTGTTATAA
ATGAACCGTGATCAGTAATGAGCCTCTCTCTCTGCTTTACAAAGAGCTTGTCGGATTGTATCGATATAGCACTGTACTGG
TCGGCTTGCCGTTTGATCACATAAGTTGGCAAAGCCTAGTAATTAAATAAAACGATCTTTGTACTAAGATCATACGACTG
TATGACTGAGCTGTTCACTAATATTGATATGCAAGCACATATATTTAACA

Align All Sequences

Map Positions (14)

Oryza sativa Japonica Group (1)

Map Type

Map Set

Name

Map

Position

Ext. Links

Sequence

Gramene Annotated Nipponbare Sequence 2009

BNL6.32

Chr. 10

16,358,895-16,359,111 bp

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Oryza sativa (13)

Map Type

Map Set

Name

Map

Position

Ext. Links

Genetic

CIAT SSR 2006

BNL6.32

10

79.3-79.3 cM

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Cornell SSR 2001

BNL6.32

10

58.3-58.3 cM

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IRMI 2003

BNL6.32

10

41.6-41.6 cM

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QTL

CAU IRAT109/YUEFU QTL 2004

BNL6.32

10a

0-0 cM

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CNHZAU Zhe97/Wuy2 QTL 2004

BNL6.32

10

28.2-28.2 cM

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CNYU Bal/Nan//Bal BC1 QTL 2001

BNL6.32

10

64.3-64.3 cM

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Cornell IR64/Azu DH QTL 2001

BNL6.32

10

58.3-58.3 cM

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Cornell Jef/Oruf BC QTL 2003

BNL6.32

10

28.3-28.3 cM

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JUT Akihi/IRAT109 QTL 2004

BNL6.32

10

28.58-28.58 cM

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LSU Caiapo/IRGC103544 QTL 2004

BNL6.32

10

22-22 cM

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M202/IR50 UCD QTL 2003

BNL6.32

10

31.3-31.3 cM

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NDSU EM93/SS18 BC QTL 2004

BNL6.32

11

136.9-136.9 cM

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TKU Integrated QTL 2002

BNL6.32

10

11.1-11.1 cM

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Associations (21)

Species	Type	Name	Assoc. Type
Oryza sativa	QTL	AQDU011	qtl_marker
Oryza sativa	QTL	AQEI016	qtl_marker
Oryza sativa	QTL	AQEI083	qtl_marker
Oryza sativa	QTL	AQEI084	qtl_marker
Oryza sativa	QTL	AQEI138	qtl_marker
Oryza sativa	QTL	AQEI147	qtl_marker
Oryza sativa	QTL	AQFE021	qtl_marker
Oryza sativa	QTL	AQFE022	qtl_marker
Oryza sativa	QTL	AQFE055	qtl_marker
Oryza sativa	QTL	AQFE080	qtl_marker
Oryza sativa	QTL	AQFJ069	qtl_marker
Oryza sativa	QTL	AQFP017	qtl_marker
Oryza sativa	QTL	AQFU012	qtl_marker
Oryza sativa	QTL	AQGP005	qtl_marker
Oryza sativa	QTL	AQJ010	qtl_marker
Oryza sativa	QTL	CQAA11	qtl_marker
Oryza sativa	QTL	CQAE13	qtl_marker
Oryza sativa Japonica Group	Primer	RM184_forward	primer_forward
Oryza sativa Japonica Group	Primer	RM184_reverse	primer_reverse
Oryza sativa	Genomic DNA	U40708	contained_in_sequence
Oryza sativa	Genomic DNA	U40708	source_sequence

Images (1)

1 IR36

2 N22

3 IR64

4 Azucena

5 Zhai-Ye-Qing 8

6 Jing-Xi 17

7 Milyang 23

8 Gihobyeo

9 Lemont

10 Teqing

11 Nipponbare

12 Kasalath

13 BS125

14 BS125/WLO2 F1

15 WLO2