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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggctgccaattacttcaatacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttttgcag

Basic information

species Zea mays
transcript GRMZM2G128877_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 13
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggctgccaattacttcaatacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttttgcag
|||| |  ||   || ||||| |||||||| || || |||||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||   || || ||                               |||  || ||||| | | ||||| | |||||| | |  ||||||| ||  || | ||| |||| ||
TCCAAAACGGGACGGAAGTGTTACAATTGTAGGGGCTGTCTCTCCACCTGGTGGTGATTTTTCAGATCCTGTTACCTCTGCAACCCTTAGTATTGTTCAGgtaaggaagcagctaa-------------------------------gtctgtcatgattaataatgtttatcgtttcagtgt--tgttaaaccacatgtt-cttgtttgtag

upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 14
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacgg--ctgccaattac---ttcaatacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttttgcag
 || ||  | || || ||||| ||||||||||| || || || || || || || ||||| ||||||||||| || |||||||||||||| || |||||||||| ||    ||  ||| ||    |  |||   | | | ||   |   |  |||   |     ||    ||  |    || |   | ||||||||| |                   
CCCTGAACGTACAGGTAGTGTAACAATTGTTGGTGCTGTTTCGCCACCTGGAGGAGATTTCTCAGACCCTGTGACATCTGCAACCCTCAGCATAGTTCAGgtaaaactattctttcaaatatggttaaaatgggtaactgcctgcaaagtaagtcagcctaaggttgtcttgacta--attcccgcaaattgttaaaaccct----------------

upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 14
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaaga---cggctgccaattacttcaatacttcagtcccccaatcat----tggtccatcctgatttaca-----------gtgtttgttgtttcaatatattgttaaatcatgtgct---gcttttttgcag------------------------------------------------------
 |||||  | |  || ||||| ||||||||||| || || || ||||| || || || |||||||| ||||| || || |||||||| |||||||| ||||| |      || |      | ||||  ||  |          || |     | ||  ||  || || | |           ||||||  | |||  || |   |   | || | |  |   || |||||                                                          
ACCAGAACGTAACGGAAGTGTTACAATTGTTGGTGCAGTTTCGCCTCCTGGAGGAGACTTTTCAGATCCTGTGACTTCAGCAACCCTTAGTATTGTGCAGgtgattatttggttcatgtctgcttccctatcttccattgtagattacatagtcgtatatgttggttgagatgaaccagatggtgtttagt-tttagatctgccgcagactcgtatatttaagcattttttttctccactttgaaatgcttactcttccattctggttgtttctcttttcttctgcag

upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 14
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggctgccaattacttcaatacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttttgcag
 |||||  | |  || ||||||||||||||||| || || |||||||| || || ||||| || || ||||| || |||||||| ||||| ||||| |||||||    | |   | |   |      ||||        ||   | |  | ||    |  || | || | |  |  ||||  | ||  |  |  |  || |    |       
ACCAGAACGTAACGGTAGTGTCACAATTGTTGGGGCTGTGTCTCCTCCTGGAGGAGATTTCTCTGATCCTGTGACATCTGCAACTCTCAGCATTGTCCAGgtaaa---gataaaattctgtatgcatcttctaatattaaaatgtag--ctattaatacgtatattggt-gaagggtcaaatttttaatgtagaaaatgatagcat-------

upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 14
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaag-acggctgccaattac--ttcaat--acttcagtcccccaatcattggtccatcctgatt---tacagtgtttgttgt----ttcaatatattgttaaatcatgtgctgc--ttttttgcag---------------
 ||  |  | ||||| ||||| || ||||||||||| || || ||||| ||||| ||||||||||||||||| ||  | || |||||  |||||||||||||  | |    | ||   |    | || |  ||  || ||  |||   |||     | ||  |     |     ||| | | |    ||  || | ||   |    | |  ||      | ||| |                
CCCGAATCGTACTGGAAGTGTTACCATTGTTGGAGCAGTGTCCCCTCCTGGTGGAGATTTTTCAGACCCTGTCACAGCAGCTACCCTTGGTATTGTTCAGgttggtatttgtacctcctctcatccagtgcaccacattctaccagatattctctaagccaaagcccatgagaagttggctatgatgttgcatgtcttccaagcgaaggaactaaagcatattgtaaatgcatgttgattag

upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 13
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggctgccaattacttcaatacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttttgcag
      ||| ||||| |||||  | ||||| || ||||| |||||||| ||||| ||||| ||||||||||||||  | || || || | |||||| |||| ||| || ||       | ||   |  ||||||       | | |||  ||   |  |||   |                                                
------CAGAACTGGAAGTGTTTCTATTGTCGGTGCCGTGTCTCCTCCTGGTGGCGATTTCTCAGACCCTGTTACGGCAGCGACTCTTAATATTGTCCAGGCAAG-Cgtctttgtgccagtt--gtttttcagtgt-----tgactgggacactgttgtttgttgcag---------------------------------------------

upper sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 13
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 14
TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggctgccaattacttcaatacttcagtcccccaatcattggtccatcctgatttacagtgtttgttgtttcaatatattgttaaatcatgtgctgcttttttgcag
       || ||||| |||||  | ||||| || ||||| |||||||| ||||| ||||| ||||||||||||||  | || || ||  ||||||| |||| ||| || ||       | ||   |  ||||||       | | |||  ||   |  |||   |                                                
------TAGAACTGGAAGTGTTTCTATTGTCGGTGCCGTGTCTCCTCCTGGTGGCGATTTCTCAGACCCTGTTACGACAGCGACTCTTGGTATTGTCCAGGCAAG-Cgtctttgtgccagttt--tttttcagtgt-----tgactgggacactgttgtttgttgcag---------------------------------------------

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|32929207|gb|CF034019.1|CF034019
EST:     GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|13149764|gb|BG320086.1|BG320086
EST:     TTACCTCCGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: TTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|32831320|gb|CD970998.1|CD970998
EST:     GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|32928400|gb|CF033212.1|CF033212
EST:     GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|74035379|gb|DT535868.1|DT535868
EST:     GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|211532168|gb|FL123442.1|FL123442
EST:     GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|211154401|gb|FL123520.1|FL123520
EST:     GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|33092495|gb|CF052489.1|CF052489
EST:     GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|32836684|gb|CD976362.1|CD976362
EST:     TTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGTAAGCATTTCCCATCT
genomic: TTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
EST: gi|67025855|gb|CO454604.1|CO454604
EST:     GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAG                         GTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT
genomic: GTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 419

TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 755

TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 599

TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 684

TCCAGACAGGACTGGCAGTGTCACAATTGTTGGAGCCGTCTCTCCTCCAGGTGGTGATTTTTCAGACCCTGTTACCTCTGCAACCCTCAGTATTGTTCAGgtaagacggc ... ttttttgcagGTCTTCTGGGGTTTAGATAAAAAGCTCGCTCAAAGGAAGCATTTCCCATCTGTGAATTGGCTCATTTCCTATTCGAAATACTCCAAG