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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGCCTTTCCGGCGGCGCTGTTGTTCGATTGCGATGGTGTGCTGGTGGACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattccttccatccgtactcccgttcatctccattttcttgatgcagctgcttccactatgttaatcttttctgcggtacctatgctcctagttat...

Basic information

species Zea mays
transcript GRMZM2G094978_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 1
CGGTGCCTTTCCGGCGGCGCTGTTGTTCGATTGCGATGGTGTGCTGGTGGACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattccttccatccgtactcccgttcatctccattttcttgatgcagctg-cttccactatgttaatct----tttctgcggtacctatgctcctagttat
||   || | |||||||||||| ||||||| ||||| || |||||||||||||| |||||||| ||||||||||| ||||||||||| || || ||||||||||  |||||||   ||    || || | || |   |||  | || ||   || |     ||  |    |||    | |  | |   | |||| |  | || | 
CGCGTCCCTCCCGGCGGCGCTGCTGTTCGACTGCGACGGCGTGCTGGTGGACACGGAGAAGGACGGCCACCGCATTTCCTTCAACGAGACGTTTGCCGAGgtccggttccttcagccc-cggtctcgctaattttggtttgat-gacgcgtttggcgattgctccgcaggtctaaagtgttggtgtcgcttatgtt--tggtaa-

upper sequence: GRMZM2G094978_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 1
CGGTGCCTTTCCGGCGGCGCTGTTGTTCGATTGCGATGGTGTGCTGGTGGACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattccttccatccgtactcccgttcatctccattttcttgatg-cagctgcttccactatgttaatcttttctgcggtacctatgctcctagttat
    ||  ||||  |||| ||  | || || || ||||| ||||| || || |||||||| ||||| || ||||||||||||||||| || ||||||||||| |  ||||||| || | | | |   ||  | |   |||| || |   |   |  ||  | |   ||  | |||| ||   |   | || |   ||||  
TTCAGCTCTTCCATCGGCTCTCCTCTTTGACTGTGATGGGGTGCTCGTCGATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttccttc-attcatccgcttatttctgttttttttttttacctcttttttttttagttaattggttttttatggaatgggtgtgttatcagttga

upper sequence: GRMZM2G094978_T02 (Zea mays), 5'ss of exon 1
lower sequence: EDP03206 (Chlamydomonas reinhardtii), 5'ss of exon 2
CGGTGCCTTTCCGGCGGCGCTGTTGTTCGATTGCGATGGTGTGCTGGTGGACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGC---CGAGgtccaattccttccatccgtactcccgttcatctccattttcttgatgcagctgcttccactatgttaatcttttctgcggtacctatgctcctagttat--
      ||  ||| || ||||| ||||||||||||| || ||||| |||||||| |||   || ||||||||||||  |||||||||  | |||     | |||      ||      || ||    | |    ||||   |   ||| |   ||| ||   |||  ||       |  |||  | |||  |          |  
------CTGCCCGACG-CGCTGCTGTTCGATTGCGACGGCGTGCTTGTGGACACGGAGCGCGACGGCCACCGCATCAGCTTCAACGAGGCGTTCAAGCGCAAGGgtgcgctcgcagtctcagtctcactgcgggtctctggtggtttggtagcgct-ctcttactgcgtggtctggtagtgcactgcctgagtggtctcccgtag

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|148972975|gb|EE024010.2|EE024010
EST:     ACACTGAAAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATT-AGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAG
EST: gi|91056651|gb|EB167069.1|EB167069
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|211135672|gb|FL156035.1|FL156035
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|211136605|gb|FL156036.1|FL156036
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|149014075|gb|EE043602.2|EE043602
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|13490397|gb|BG517161.1|BG517161
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|149112364|gb|EE295251.2|EE295251
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|211136608|gb|FL156039.1|FL156039
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|50333792|gb|CO528918.1|CO528918
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|211136612|gb|FL156043.1|FL156043
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCCCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|211136613|gb|FL156044.1|FL156044
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|211136615|gb|FL156046.1|FL156046
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|13558960|gb|BG550315.1|BG550315
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|94479515|gb|EB708473.1|EB708473
EST:     ACTGAGAAGGATGGCCCCCGCATCTCCCTTCA-CGAAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACTGAGAAGGATGGCCACCGCATCTCC-TTCAACGAAA-CCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|86467369|gb|DY233739.1|DY233739
EST:     ACACTGAAAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCAGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAAAATTGCTCAAG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAG                         AGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG
genomic: ACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattcc ... atatttacagAGGGAATTAGGTGTCAGCTGGGATGTTGAACTGTATGGAGAATTGCTCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTGCCTTTCCGGCGGCGCTGTTGTTCGATTGCGATGGTGTGCTGGTGGACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattccttccatccgtactcccgttcatctccattttcttgatgcagctgcttccactatgttaatcttttctgcggtacctatgctcctagttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG