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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA

Basic information

species Oryza sativa
transcript LOC_Os05g51530.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G128995_T05 (Zea mays), 3'ss of exon 5
-------------gtagattgcatgccactgagtttttg-------gctttaagcca--attctttcttgttttatttcaaaggactcagaaatgcgagggt--atggtttcatc-ttttgttagtcaact--------ctaattagtttgttttccttctgtat---agCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA-----
               | | |   ||         | | |       |||| |  |||  | | |||| |  ||||||  ||| |   ||| |  ||     |  |||| ||  || |||| |  ||   ||        ||||||||||||   |  |  ||| |   |||||||| ||||||||||||||||||||||||||||| ||||||||| |||| || |||||||| |||||||| |||||| ||||||| |||||||| |||     
gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 5
------------------gtagattgcatgccactgag----tttttggctttaagccaatt-----ctttcttgttttatttcaaaggactcagaaatgcgag-------ggtatg---gtttcatcttttgttagtcaactctaattagtttgttttcc-ttctgt-atagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA
                   |    ||||  ||   |||    | ||||     ||| | |||      |  |||||||  ||| ||| |   ||| |  |||         |||||     |||||||| ||| |   |    ||||||||||||| ||   || ||| | |||||||| ||||||||||||||||||||||||||||| ||||||||| |||| || |||||||| |||||||| |||||| | ||||| |||||||| |||
gtaaattgcattgtcatacttttgtgcagaccctggaggaactgtttgatgccaagaccattacgttttcccttgtttattttaaaaaggaacaggagagcggaactggatggtatatccatttcatctgttgctttcctgtactaattagtttgtcttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 5
gtagattgcatgccactgagtttttggctttaagccaattctttc-ttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgt-tttccttctgt-atagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA
                                   |||||| ||  |||||||||  ||||| |   || || ||   | || |  |  |    || ||  |   | || |||||||||| ||| ||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||   ||||| |||||||| ||||| |||||  ||||||| |||||||| |||
----------------------------------tcaattcctttgttgttttatg-caaagcaagtaggaaggcagagttagg--tcaactgcttcttgttatgcactgattagtttgtgttttcttctgtgacagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTGCTCAGAGCATCTAGTAACACTTCTTGCTATTGTTCCAAAGTACTCCCAA

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 5
-------------gtagattgcatgccactgagtttttg-------gctttaagcca--attctttcttgttttatttcaaaggactcagaaatgcgagggt--atggtttcatc-ttttgttagtcaact--------ctaattagtttgttttccttctgtat---agCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA
               | | |   ||         | | |       |||| |  |||  | | |||| |  ||||||  ||| |   ||| |  ||     |  |||| ||  || |||| |  ||   ||        ||||||||||||   |  |  ||| |   |||||||| ||||||||||||||||||||||||||||| ||||||||| |||| || |||||||| |||||||| |||||| ||||||| |||||||| |||
gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 5
gtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA
                                          |   |||| | | |  ||  |    ||  |   |   ||     | |   ||| ||||   ||| |||| |   | ||| |||  | ||  ||||||| || ||||||||||||||  |||||||||| ||||||||  | || |||||| || ||   || || |||||| ||||||| ||||| || || 
---------------------------------------gtgtgaatgttatttattgaacaatcatgactttttaatataa----taagtatttcttagctgactttaatga-cctatttgcctgtttta--gCTTAGCTGTCCGTGATCTTTCCAACTTGGTAAAACCTGAGGATATTATAACTTCAGAAAATTTAACCACCCTTCTTGCAATTGTTCCCAAGTATTCACAG

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 5
gtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA
                                         ||     | || ||   |  |    ||   |   |   ||| || |  ||||||  |   |    ||| ||   |  ||            ||||||||||| ||||||||||||||  |||||||||| || || || || || |||||| || ||   || ||||||||| ||||| | ||||| || || 
---------------------------------------gtttgtggatgttgttatgactggtctagttttctaa---tatagtatattctttttctttgctgacctacttgactattt-----------cagCTTAGCAGTCCGTGATCTTTCCAACTTGGTAAAACCTGAAGACATTGTAACTTCAGAAAATTTAACTACCCTCCTTGCAATTGTTTCCAAGTATTCACAG

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 5
gtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA
                                       |   | ||||| |   |   |    |   ||||      ||||| | |  |  |||| |  || ||| | | || ||                ||||||||||| ||||||||||||||  |||||||||| ||||| || || || |||||| || ||   || ||||||||| ||||| | ||||| || || 
----------------------------------gtgtgtggatgttgttatgactggtatagttttcaaatata---gtatgttctatttctttgctgatctact-tgactatttc---------------agCTTAGCAGTCCGTGATCTTTCCAACTTGGTAAAACCTGAGGACATTGTAACTTCAGAAAATTTAACTACCCTCCTTGCAATTGTTTCCAAGTATTCACAG

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 5
gtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagt-caactctaattagtttgttttccttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA
                                              |   ||  || |||    |  | |   | |    | | ||| || |  ||| | | |   ||| ||     | ||| | | ||  |  || |||| ||||||||||||||||| || ||||| |||||||| ||  |  | ||||||||| |||||||||| |||||| ||||||| ||||| ||||| 
-------------------------------------------gtataccttggttgaaatctgtttgtaggacaaa--caagattttatttactgtgatttcttttctgatcgacctctttgcttgcttca--gCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGCCTCAGAACATTTAGTGACACTTCTTGCAATTGTTCCCAAGTATTCTCAG

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|29656670|gb|CB652945.1|CB652945
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|29662007|gb|CB658282.1|CB658282
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|29612869|gb|CB617882.1|CB617882
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58667113|gb|CK055799.1|CK055799
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCA
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCA
EST: gi|58666270|gb|CK054956.1|CK054956
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|218479849|gb|FG959490.1|FG959490
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|218498003|gb|FG943208.1|FG943208
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|29674593|gb|CB670868.1|CB670868
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|25802832|gb|CA758793.1|CA758793
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58686384|gb|CK075071.1|CK075071
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58594698|gb|CF993006.1|CF993006
EST:     ATAATGCTCAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTGGCCAATCTGGTAAAACCAGAGGATATGGTCA
genomic: ATAATG-TAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTT-CCAATCTGGTAAAACCAGAGGATATGGTCA
EST: gi|58600826|gb|CK011354.1|CK011354
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTT
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTT
EST: gi|29613101|gb|CB618114.1|CB618114
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58596246|gb|CK006774.1|CK006774
EST:     CATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|58688997|gb|CK077684.1|CK077684
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAA
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAA
EST: gi|27578007|gb|CB000702.1|CB000702
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
EST: gi|29613962|gb|CB618975.1|CB618975
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgca ... ttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA
                         ctctaat  putative branch site (score: 3)
                                   tttgttttccttctgt  putative PPT
                            taattagtttgtttt  TA-rich tract