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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag

Basic information

species Oryza sativa
transcript LOC_Os01g01710.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G056975_T02 (Zea mays), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatg--------------gaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag
||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||| |||||||||||||||||| |||||||||||||||| |||| | || || |||               | | ||||| ||   || ||| ||  || ||||  |  || ||||  ||   || || ||||||                                                                                  
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAACCCAGgtgagccctaaaccatagttatatgttttactaaaaagcacatgttgaggtattctgcccagatgtagtgcttcatacactga-aacatatccaaacttaa----------------------------------------------------------------------------------

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G036290_T01 (Zea mays), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatg--------------gaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag
|||||||||||| |||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||||||||||||||| |||||||||||||||| |||  | ||  | | |               | | ||||| ||   || | | ||  || ||||  || || |||   ||   || ||  |||||||                                                                                
AGAAGTTATTGAGGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAATCTATCATACACTCTATGGTTGAAACCCAGgtgagccctgaaccatggttgtatcttttactaaaacgcacatgttgaggtattctacccagatgtagtgctttgtacact---aacatatccatgcttaatc--------------------------------------------------------------------------------

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA05G02190.1 (Glycine max), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcaca--cttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag
|||||| |||||||||||||| || ||||| ||||| |||||| | ||||| ||||| || || |||||||| |||||||| || ||||||||||| |||||     ||| |    |  | |     |||||            | ||   |  |  ||||  |  ||  |||| |||   |  | || | |  | | |  |   ||                                                                
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTACGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgt-----cta-aatctaattctatgttatgttggttaccgcattttaatatccatatatttgga--tgcaaatggatgaggaaccatagtacctacaagctacaagtt---------------------------------------------------------------

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA17G09740.1 (Glycine max), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag
|||||| |||||||||||||| || ||||| ||||| || ||| | ||||| ||||| || || |||||||| |||||||| || ||||||||||| |||||         | |     | |     |||||||  |  |    |  |   |  |  |||   |  |   |||| |||   |   |     |  || ||| |   |  |||  |                                                       
AGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTATGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAACACAGgtata------aaccttattctatgttatgtttactgcat---tttgatatccatatattcgga--tacaaatggatgaggaacca---tagccatagcacctacaagttccag-------------------------------------------------------

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 5'ss of exon 9
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag
|||||||||||||||||| ||| | ||||| |||||||| ||||| ||||| ||  | || || ||||||||||||||||| |||||| | ||||| ||||| | |           | |||         |||  |  |  |||       | |   ||| | |     ||| |   || |  |  | |  || |   |   |   ||||    ||| || |     |    ||| | || ||                         
AGAAGTTATTGAAGCACACTATCTGTTTGGGGCTGAATATGATGATATTGAGATCATAATTCATCCACAATCTATCATACATTCTATGGTCGAAACACAGgttaatt----------gttat--------cttattgtcttggcttcttcttaatatgtttaagatgtcaaataccatcagaactgtttcatattttttagaagcggtttc----ttatgtcttctccacccctttctctccag-------------------------

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S62_157V6.2 (Physcomitrella patens), 5'ss of exon 11
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggatttta---aactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag
 ||||| |||||||| || ||| | || |||||||| |||||||||||||| |||||  |||| || ||||| ||||| || || ||| | || || ||||| | ||  |      |  | | ||   | |||       ||     | |       | || |   |    | |     |  ||  ||  |  ||  |         ||   |  || | || | |||  | || | | | | |     || ||                  
GGAAGTGATTGAAGCTCACTATCTCTTCGGTGCTGATTACGATGACATTGATATTGTTGTCCATCCCCAATCAATCATTCATTCCATGGTGGAGACACAGgtaactctcatgtttgacatgtagattttttttccaaaccatttgtgaataggtcatagttcaccaagagctcagaatgtagacttttgcttttgtcacattggttatacaat--tgctgacttctgggatgatgtctgtatcctctgttttatag----------------

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ09183 (Selaginella moellendorffii), 5'ss of exon 10
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag
 || || |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| || ||||| || |||||||| ||||| || || ||||| |        | |  |||     | |    || |     |  |||| | |||                                                                                                                   
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGACACAGgtaatatgagttgaat-gcttcaacacacaactaacacagctagtcaaatacag-------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ07179 (Selaginella moellendorffii), 5'ss of exon 10
AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggcaaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccag
 || || |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||||| || ||||| || |||||||| ||||| || || ||||| |        | |  |||     | |    || |     |  |||| | |||                                                                                                                   
CGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGACACAGgtaatatgagttgaat-gcttcaacacacaactaacacagctagtcaaatacag-------------------------------------------------------------------------------------------------------------------

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|86898927|gb|CI296156.1|CI296156
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|29613665|gb|CB618678.1|CB618678
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|29620640|gb|CB625651.1|CB625651
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|58687978|gb|CK076665.1|CK076665
EST:     CACAATTTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: CACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|14982024|gb|BI306702.1|BI306702
EST:     AATTGTGATCCACCCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AATTGTGATCCA-CCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|29688465|gb|CB684740.1|CB684740
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|58674748|gb|CK063435.1|CK063435
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|29620627|gb|CB625638.1|CB625638
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|58696138|gb|CK084825.1|CK084825
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|29620628|gb|CB625639.1|CB625639
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|86502359|gb|CI144992.1|CI144992
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|58694512|gb|CK083199.1|CK083199
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGT
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGT
EST: gi|38475522|gb|CF959655.1|CF959655
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|29620642|gb|CB625653.1|CB625653
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|29617050|gb|CB622062.1|CB622062
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|58594821|gb|CF993129.1|CF993129
EST:     AATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|58594695|gb|CF993003.1|CF993003
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC
EST: gi|58595068|gb|CF993376.1|CF993376
EST:     AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAG                         GATTCATCTGTGTTGGCTCAACGGGGATGGCCAGATATGCGGATACCAATC
genomic: AAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATC

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: 68 (upstream exon), 73 (downstream exon)
Score: 38

AGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAACCCAGgtgagtccta ... gtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATCTTATACACCATGTCTTGGCCAGACAGAATCTATTGCTCAGAGGTCACCT




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