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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os07g37740.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 12
ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag
|| ||||||||||||||||||||| |||||||  | ||||||||||| ||||||||||| ||||||||||||  | | | || |||    ||      |     |  | |   |  | |  |||     |      | | ||        |                                                                                                                
ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagtttt-ctattatcaaccgttctaattttcctgaacca-acttcagtgtgacatacttgagccctttttggaccgcgtgcag---------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA13G31830.1 (Glycine max), 5'ss of exon 13
ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag
|| |||||||||||||||||||||||||||||| | ||| ||||| ||||  |||||||||| |||||  |          || | | |   |     |||   |   |   |     ||||| |        |    |  |  | |  |||     |||| |     |     || |  |   ||| |                                                                          
ATTTTCTACTTTGTTGGATTTGGATTGTTCTGCATTGAAACATTGATCAGTGTCTGGGTTATTCAGgtttg----------aatatacatctcaatttttttggaaagtggaaacacttagcact--------ttgactgaacataaccaaa---gtacatgttcactttttttgtttgtttgcatacag-------------------------------------------------------------------------

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA13G25460.1 (Glycine max), 5'ss of exon 11
ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag
|||||||||||  |||||||||||||||||||||| ||| | ||| ||||||| |||||||| |||||  | | | |   |    ||   |||   | | | |       | |    | ||||||    ||   |||  |  |  | || |||    |||||       |  |  |||| |  | |   |   ||                                                                    
ATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAGgtttgac-tacacttcttgaactttccaatcatcttaagc----acatgcaccagcattttgaatgc-catg-atttccttatgaattaccacataccaactcactatttctt-tggtttgctatacag--------------------------------------------------------------------

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA15G07480.2 (Glycine max), 5'ss of exon 11
ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag
|| |||||||||||||||||||||||||||||| | ||| ||||| |||| ||||||||||| |||||  |          || | | |         |||   |   |   | |   ||||| |     |   ||||   |    | | ||| |  || | | ||| | |     | || |                                                                                 
ATTTTCTACTTTGTTGGATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAGgttcg----------aatatacatctgaatatttttggaaagtggaaatacttagcactttgactgaacata---accaaagttaatgttcactt-tttgtttggttg--catacag--------------------------------------------------------------------------------

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA07G31090.3 (Glycine max), 5'ss of exon 11
ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag
|| |||||||| |||||||||||||| |||||| | ||| | ||| ||||||| ||||| || |||||  |   | |   |    ||   | |   | | |       ||||    || | ||        | | | || ||| |   ||   | | | |  | |    |     |||| |  | |   |   ||                                                                    
ATTTTCTACTTCGTTGGATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAGgtttgat-tacacttcttgaactttacaatcatct-------taagcacatccaccaccattttgaatgacat-gatttcctta---cgacatacctctactcactgtttctt-tggtttgctatacag--------------------------------------------------------------------

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT1G61250.1 (Arabidopsis thaliana), 5'ss of exon 11
ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctgcgaataacaaatactccctccgtttcatattataagactttcta-gcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag
|| ||||||||  |||| |||| ||| |||||| |||||||| || | |||||||||||||| |||||| |||     ||         |||||  |  |  ||||||| || ||||  |   | ||     ||   ||   || |   |   | | |   | | |   | ||                                                                                           
ATATTCTACTTCATTGGGTTTGCATTTTTCTGCCTCGAATCAGTGGTTAGCATCTGGGTTATTCAGgtctgtctcttcaa---------ctcccatcact--atattatcagtctttgaacatagtgttataatctgtactcatttcttttggtatgggtttgttttgttggagcag---------------------------------------------------------------------------------------

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 5'ss of exon 12
ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag
|||||||||||  |||| |||||| ||||||| || |||||| ||||||||||||||||||| ||||||   | |     |  ||     | |||     |||      |||  |  ||| |  |||  |||     ||  ||  |   |  ||| |     ||| |||      ||   |  | |  |                                                                          
ATCTTCTACTTCATTGGGTTTGGAATGTTCTGTGTTGAATCAGTGCTCAGCATCTGGGTTATTCAGgtccaacttctctttccca-----ttcctaataatcacg--gaaagcatagctacctctgctaata---ggatgaatcatg-cagctcttgttcactgtttctgttgtttcacctggtttgcag-------------------------------------------------------------------------

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 5'ss of exon 11
ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgt-cagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcag
|| |||||| || |||||||||||||||||||| | |||||| ||||||| ||||||||| | ||||| ||||  |  || |      || | | || | ||| |||    ||   |||||      |     ||| | ||  | |   |   |||  |      | |  ||                                                                                            
ATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAGgttcagtagtctgatt----tctagttcttctgcttc-tatctccagcacttctactgcatcttggtttcttctaactctctttgt-tctcaatcccaatatgcag--------------------------------------------------------------------------------------------

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|86430196|gb|CI082619.1|CI082619
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|3761419|gb|C98667.1|C98667
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|88970336|gb|CI383838.1|CI383838
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|87030942|gb|CI268093.1|CI268093
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|88225839|gb|CI225755.1|CI225755
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|66923956|gb|CX110804.1|CX110804
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|86429939|gb|CI082362.1|CI082362
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|44672791|gb|CR286225.1|CR286225
EST:     CTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: CTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|87027955|gb|CI276311.1|CI276311
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|58683369|gb|CK072056.1|CK072056
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|88969834|gb|CI383336.1|CI383336
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|88966183|gb|CI013059.1|CI013059
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|88269399|gb|CI380697.1|CI380697
EST:     CTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: CTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
EST: gi|88834932|gb|CI370235.1|CI370235
EST:     GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAG                         CAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT
genomic: GATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 24 (upstream exon), 75 (downstream exon)
Score: 13

ATCTTCTACTTTGTTGGATTTGGATTGTTCTGCGTCGAATCATTGCTCAGCATCTGGGTTATCCAGgtcagtcctg ... gtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAATTATCAGAAAAGA




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