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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgttatgtgcctagcatacagtgcttacatctcttagcgagagtttgtctcaaaaaagttcctcattttgtaagttcactaatatgatctattccacag

Basic information

species Zea mays
transcript GRMZM2G010202_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 5'ss of exon 10
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgttatgtgcctagcatacagtgcttacatctct----tagcgagagtttgtctcaa-aaaagttcctcattttgtaagttcactaatatgat----ctattccacag------
|||||| ||||||||||| || || || |||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||   || |||| |  |     |  |   | ||    |     |  |||  | |  ||  |     | | ||| | | |   |  ||  |    |  ||||     || || ||| |||        || || |       
TTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttcttcaataactaataattcattgttttagttttgaattcggtaatacacccagaatctcttctattaattgcaaattttttttctgattgaccaatgtgacaacatattttcataattctag

upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 5'ss of exon 10
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgttatgtgcctagcatacagtgcttacatctcttagcgagagtttgtctcaaaaaagttcctca-------ttttgtaagttcactaatatgatctattccacag------
|||||| ||||||||||| ||||| || || ||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||   ||||||| |||    ||   |   | |  |  | |  | |   |||||   | |   | | ||    |  | || | || ||| |||       || ||    || |||||| |||  | || || |       
TTTTGAAGTTCTTGGAGACAATGACTCGCCGGTCATGCCTATCATGCTTTACAATCCTGCTAAAATACCTGCGTTCTCAAGAGAGTGCCTGAGGCAACACgtgagttttca----aaatatacctcacctaacgaataaatcatgctttagttttgaatccag----tagcacacataatttcttcactgaaaattctgctgtttgactaatgtgacatgtttcataattctag

upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 10
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgt-tatgtgcctagcatacagtgcttacatctcttagcga-gagtttgtctcaaaaaagttcctcattttgtaagttcactaatatgatctattccacag
 |||||||||||||| ||||||||||| || || ||||| |||||||||||||| || || ||||| ||||| || ||||| |||||||| | |||   ||||||  |    |  | ||  || | ||||  ||| |   | |   | ||||||   ||   | || |||||   ||  ||  |   || ||| | | ||||                     
ATTTGAGGTTCTTGGGGATAATGATTCTCCAGTAATGCCAATCATGCTTTACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacatcaaatatccaactatctatgctccttgttgata--ccctacatcatataagaatgaatttgt--taattaatgtttacaattttttatttcag--------------------

upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G26210.1 (Glycine max), 5'ss of exon 10
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcata-caaaccgtctgttatgtgcctagcatacagtgcttacatctcttagcgagagtttgtctcaaaaaagttcctcattttgtaagttcactaatatgatctattccacag
 |||||||||||||| ||||||||||| || || ||||| |||||||||||||| || || ||||| ||||| |||||||| |||||||| | |||   ||| || ||  | | | |||  | || |   || |    ||||  | | | ||| | | ||   ||  |||| | |  || |||   |||||| | | ||||                     
ATTTGAGGTTCTTGGGGATAATGATTCTCCAGTAATGCCAATCATGCTTTACAACCCCGCCAAAATCCCTGCCTTCTCAAGAGAGTGCCTCAAGCAGAATgtaagatcaaacatccaactttatgctccttgtcg---ataccctacat-catgtataagaatgaaattgt-taatcaatgtttaccatttt-tgaattcag--------------------

upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT5G23670.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttct--catacaaa-ccgtctgttatgtgcctagcatacagtgcttacatctcttagcgagagtttgtctcaaaaaagttcctcattttgtaagttcactaata---tgatctattccacag
 |||||||| |||||||| |||||||| || ||||||||||| ||||||||||| || || ||||| || || |||||||| || || ||| | |||   || ||||||   || |||| ||   | | || ||   || |  |  |  | |||     || | |||     ||  |||  |  |  | |  ||||  || || |   |   |||     |  ||||
ATTTGAGGTACTTGGAGACAATGATTCCCCAGTCATGCCTATAATGCTTTACAACCCAGCAAAAATCCCAGCTTTCTCAAGAGAATGTCTGCGACAAAAAgtaagttctattattcaaatccaaatatcatatg---agaactcgat--taacacaaggtaacaaga-----tcaaaaagtaaatgattaacttgtgggtgcaatggaaccttgaaactctgaacag

upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT3G48780.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgttatgtgcctagcatacagtgcttacatctcttagcgagagtttgtctcaaaaaagttcctcattttgtaagttcactaatatgatctattccacag
 ||||| ||||||||||| ||||||||||| |||||||| || |||||||||||||| || |||||||| |||||||||||||| ||  || |  ||   || ||||             ||| ||   |  ||   | | | |  ||     | || ||     ||   | ||| | | |  |    | |||        ||||   || | |   ||||
GTTTGAAGTTCTTGGAGACAATGATTCACCAGTCATGCCAATAATGCTTTACAATCCAGCAAAAATTCCAGCATTCTCAAGGGAATGTTTGCGAGAAAACgttagtt-------------tctcttgcttttct--taaaaaatattt----ttttttgc-----ttccacacaagagactcacctcctatgttcaacggataatgaaatttgtga-acag

upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 5'ss of exon 11
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgttatgtgcctagcatacagtgcttacatctcttagcgagagt--ttgtctcaaaaaagttcctcat--tttgtaagttcactaatatgatctattccacag-----------------------------------------------
 |||||||||||||||||||||||||| ||||| ||||| || |||||||||||||| || ||||||||||| || ||  ||||||| || |  ||   ||| || | |      ||     |  |||      | ||| ||   |||     ||||    | |||   ||    | | |  ||||   |  ||  |  ||  |  | |      || ||  |||                                               
CTTTGAGGTTCTTGGAGATAATGATTCTCCTGTAATGCCAATAATGCTTTACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagctttatctttaat----ttctatacattcaccattcatgtcttttcattcttgattaaagtagctgcaatacagagattccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggctagtattgacaagttatgctgttccag

upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 5'ss of exon 10
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttc-tcatacaaaccgtctgttatgtgcctagcat-acagtgcttacatctcttagcgagagtttgtctcaaaaaagttcctcattttgta-agttca--ctaatatgat--ctattccacag--------------------
||||||||||||||| |||||||| || || || ||||| || |||||||| |||||||  ||||||||||| |||||  | |||||||| | ||||  ||||||| | |||    |  |   |||  | |  |||  || |      |     || |||||    || | | |   |   || | |||  | | | |||| |  || || | ||  || ||   ||                     
TTTTGAGGTTCTTGGGGATAATGACTCTCCAGTGATGCCAATAATGCTTTATAATCCTGGCAAAATTCCTGCCTTCTCGCGAGAGTGCCTCAAGCAAAATgtgagtccatcaagacatgcacgtgtcctataactatgattattccattctggacttttagctcatgtctatat--gacctgtccttcaaatggcacagtttattctcatttcatggctttttatcaaagtcaatggtgctgttacag

upper sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
lower sequence: PP1S377_35V6.1 (Physcomitrella patens), 5'ss of exon 10
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgttatgtgcctagcatacagtgcttacatctcttagcgagagtttgtctcaaaaaagttcctcattttgtaagttcactaatatgatctattccacag
|||||| ||  | || || |  |||||||||||||||||| ||||||||||||| ||||  || ||||| || |||||  |||| ||||| | ||     || ||   | |  | || |  ||   |  | || | ||  |  || | | || ||      |    |  |||  |   | |    | ||||      ||   | |                
TTTTGAAGTCTTGGGTGACATGGATTCACCTGTCATGCCTGTCATGCTTTACAACCCTGGAAAGATTCCAGCCTTCTCTCGGGAATGCCTCAAGCGCAACgtaagaa-ttactcgaatc--ctaccacattcccatca-gctttggtca-atttcgatttaacttgtattcttgatgtaatattcctttttaaggagtccaaagt----------------

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|71445384|gb|DR826434.1|DR826434
EST:     ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCT                         GTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
genomic: ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctc ... tattccacagGTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
EST: gi|86467008|gb|DY233378.1|DY233378
EST:     ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCT                         GTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
genomic: ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctc ... tattccacagGTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
EST: gi|148947745|gb|EC893228.2|EC893228
EST:     ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCT                         GTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
genomic: ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctc ... tattccacagGTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
EST: gi|37374692|gb|CF623727.1|CF623727
EST:     CTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCT                         GTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
genomic: CTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctc ... tattccacagGTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
EST: gi|211322417|gb|FL451105.1|FL451105
EST:     ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCT                         GTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
genomic: ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctc ... tattccacagGTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
EST: gi|211322418|gb|FL451106.1|FL451106
EST:     ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCT                         GTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA
genomic: ACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctc ... tattccacagGTTGCTGTTGTTACTGTTGCATTTCCTGCCACGCCACTTCTACTTGCGAGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgttatgtgcctagcatacagtgcttacatctcttagcgagagtttgtctcaaaaaagttcctcattttgtaagttcactaatatgatctattccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT