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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag

Basic information

species Oryza sativa
transcript LOC_Os09g07510.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 4
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacata-----taatatttatttgca-gacattcattagttgctagaggttcctga----tgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactc--attaaatag------------------
 ||  | ||||||||||| || ||||||||||||||||| |||||||| || |||||||||| ||||||||| || ||||||||||| |||||||| |||||| ||   || |    |||||  || | |      |    || |  | | |      |||| | |||  |   | | | | |||  |  |||  | | | |    |||| | ||    |  | |  | ||  | |   | |  |    | | |  |   |   | | |   |||   ||                   
GCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGTAAATTTCTCTCAGgtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaaaattactaga-gtaagatttccataagatctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgttttcttaacatctcag

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA07G10000.1 (Glycine max), 5'ss of exon 3
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
 ||  |  | || ||||| || ||||| ||||| || |||||||||||||| ||||||||||| |||||||| ||||| || || |||||||| || |||||   ||   ||  || |   |||     |   || ||  |      | ||   | || |||   |  | || ||||   ||    |   |  ||| |    |  ||                                                              
TCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGAAAATTGTTGGAACCTCAAGATTGTGTGGCACATATTCTTCCTGTCATAGTCAATTTTTCTCAGgtttgttg-gccattagt-aatacactgatactatatatgtag----agattagagatatatcctcc-atatccattttgtggccaacactaatgaggggatgtctt--------------------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G10790.1 (Glycine max), 5'ss of exon 4
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
  | |||||||| || || || |||||||||||||||||| || |||| |||||||||||  |  ||||||| || || ||||||||||| ||||| |||||  |||          || | |    | | |   ||  | | |||||   |    |||| | |||     |||||||  ||||  |   |  || |    | |||    |    | |                                                   
TAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGGTTATTGTCAACTTCTCGCAGgtgtatt---------tttagcagtgaaatat--actgttagttatcatcaaattaatttttctgc-----ttcatta--tgcttaaaactattgctttatctagtaatgttcagttt---------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 4
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatata-atatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
  | |||||||| || || ||||||||||||||||| ||  ||||||| |||||||||||||| |||||||| || || |||||||| || |||||||||||| || | |     |||   ||  |   | | || ||  | |||| | ||||| ||| | |    ||  | |    || |||  | |||         |    |                                                                 
CAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAGgtacatgatagg--aactgtatatatatatat-atatatat-atat-atatatatataatgagagacaagcttctgatatttggaataggaaaacagaacgataa-----------------------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 4
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
  | |||||||| || || ||||||||||||||||| ||  ||||||| |||||||||||||| |||||||| || || |||||||| || |||||||||||| || | |     ||| | ||  |   | | || |||       |||| |||     ||  | | || |||       |   | |      ||||    | |||                                                               
CAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAGgtacatgatagg--aactggatatatatatat-atatacacacacacacagatatatactagcttctgatatttg--gaataggaaaacagaatgataaaac-agt---------------------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G31760.1 (Glycine max), 5'ss of exon 4
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaatta--cacccctact--tggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
 ||  |  | || ||||| || ||||| ||||| ||||||||||||||||| |||||||| || |||||||| ||||| || || |||||||| || |||||   ||   ||    || |  || |||     |   || ||  |      | |    |  | ||| | |  | || ||||  ||| | |      || |||    ||                                                                 
TCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGGAAATTGTTGGAACCTCAAGATTGCGTGGCACATATTCTTCCTGTCATAGTCAATTTTTCTCAGgtttgttggccattagtaatactgatacactgatactatatatgtag----agactagaggtatatcttcc-atatccatt--ttg-tggccaacactaatgagagga-----------------------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 4
-------------ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
               | |||||||| || || || |||||||||||||||||| || |||| |||||||||||  |  ||||||| || || ||||||||||| ||||| |||||  |||          || | |    | | |   ||  | | |||||   |    |||| | |||     |||||||  ||||  |   |  || |                                                                        
ATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGgttattgtcaacttctcgcaggtgtatt---------tttagcagtgaaatat--actgttagttatcatcaaattaatttttctgc-----ttcatta--tgcttaaaactattgct------------------------------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 5'ss of exon 3
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
  | || ||||| ||||| || |||||||||||||||||||||||||| || || ||||||||   ||| || ||||| || ||||| |||||||| ||||| | |||   |  ||       | |   ||      |  |    | | |   |||  ||| |    |   ||  | | |    ||                                                                                   
TAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGTTAATTTCTCGCAGgtga-ttatgtctgtag-----gcttttatgctgatgatctacatttaaaagaaatgcttaatctttgtactttttcactgagcag-----------------------------------------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 4
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaatta-cacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
  | || ||||| ||||| || |||||||||||||||||||||||||| || || || ||||| ||||| || ||||| || |||||||||||||| ||||||||| |        |  || ||    | |   ||  | |     | |     ||  | ||   ||||| ||  || || ||||  |   || ||||  |    ||   ||  |  |                                                    
TAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGTCAATTTCTCGCAGgtaaataaatgtgtgaatatgataaaaaaattctattga-tgagctttatgggaaagctgtaag-gcagatatgtatgagctgcttta---tcttgatttttttcgtc-tttgagcag----------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 4
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctca-gtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
  |  | ||||| |||||||| ||||| |||||||| || ||||||||||| || |||||||| ||||  ||  | || |||||||| |||||||| ||||| ||||   |      ||  |   ||| |  |  |  | || ||      | |  | ||   |     |  |||||  ||    | | |  | || || || ||  |  |||| | || | |||    ||  || ||| | |                           
GAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGTTAATTTCTCTCAGgtgaattgagctttgtttttttcattcatggatttttcagttaat----tgtctgctgttccatgtttaattttcatcggt----aaaag--cttgctgttctgatgtttttctatggtgtttgtattgat--ttctgagagcag-------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv03s0038g00200.t01 (Vitis vinifera), 5'ss of exon 1
---------------------------------------ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTA-TTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
                                         | || ||||| ||| | || ||||| ||||| || ||| |||||||||| |||||||||||||||||||| |||||  | | || | |||||||| |||                                                                                                                                                                         
AATATTTGAGGATCTGACACAGGATGATCAAGATTCTGTTAGGTTATTGGCTGTTAAGGGTTGTGCAGCTCTCGGAAAACTGTTGGAACCTCAAGATTGTgtagcacatattcttcccataaattatgaatttctctcag-------------------------------------------------------------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 5
ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
  | || ||||| ||||| || ||||| ||||| || ||  |||||||||| |||||||||||||||||||| ||||| || ||||| |||||||| |||||| ||                 ||  |  ||         |||||   |   || |||||||| ||   |||   |  ||  ||     |  | | | | |   |    |   |  ||||||||    |                                       
TAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAAAGCTGTTGGAACCTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGTGAATTTCTCTCAGgtacat-----------------ccataaagttg-------gatatgttaatcaacatttatttccatggatttgcttattcata-----ttttaaagtttctt-tgatcttcatcttatgtgttcaagt---------------------------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv04s0008g07090.t01 (Vitis vinifera), 5'ss of exon 2
-----------------------------------------ACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatag
                                           | || ||||| ||| | || ||||| ||||| || ||| |||||||||| ||||||||||||||||||||   |     ||     || | ||     ||| |    |     |  ||||   | ||   | |  | | |  |||| ||  |   ||||     |                                                                                                      
TCAATATTTGAGGATCTGACACAGGATGATCAAGATTCTATTAGGTTATTGGCTGTTAAGGGTTGTGCAGCTCTCGGAAAACTGTTGGAACCTCAAGATTgtgtagcacatattgatt--actaccaaaaagtgctattttgtagacctaataataa--tggt-tttaagcacctttgaatagtaatcatattca---tttaacccaa------------------------------------------------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|300215963|gb|HO088589.1|HO088589
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|58654414|gb|CK043094.1|CK043094
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|58652709|gb|CK041389.1|CK041389
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|33654809|gb|CF277423.1|CF277423
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCA-                         GAC-AAT-ATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|58593044|gb|CF991352.1|CF991352
EST:     AATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATAGTGGTTGCCAATCAATTGTATGAGCT
genomic: AATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATA-TGGTTGCCAATCAATTGTATGAGCT
EST: gi|33796143|gb|CF323937.1|CF323937
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|58672176|gb|CK060862.1|CK060862
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCG
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCG
EST: gi|300215769|gb|HO088395.1|HO088395
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
EST: gi|33676187|gb|CF304426.1|CF304426
EST:     CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAG                         GACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC
genomic: CACAAGATTGTGTAGCACATATCCTTCCAGTTATTGTCAATTTCTCCCAGgtaaattaca ... cattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTC