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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCCCGACGGCGACGTCATCCACTGCGTGCCGGCGCACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaaatcccttgctctacctagcatctagcattagcaagcaccgccgtttcgttctggatctgttccgcggtcgacggagtgtcctgagcaacgtgcgtgtgtgcaattgtgcatcgctcccag

Basic information

species Zea mays
transcript GRMZM2G162928_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162928_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g07570.1 (Oryza sativa), 5'ss of exon 2
AGCCCCGACGGCGACGTCATCCACTGCGTGCCGGCGCACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaa-aatcccttgctct--acctagcatctagcattagcaagcaccgccgtttcgttctggatctgttccgcggtcgacggagtgtcctgagcaacgtgcgtgtgtgcaattgtgcatcgctcccag
|||||||||||||| |||||| |||||||||||||||||||||||||||||||||| ||||| | |||| |||| ||| |||||||||||| | |  ||||| ||| |||  |  |  | | | |  || |      | |   |    |||||  |||||  |   |||| ||    || ||       ||  ||| | |    ||||||          
AGCCCCGACGGCGATGTCATCGACTGCGTGCCGGCGCACCTGCAGCCGGCGTTCGAGCACCCGAAGCTGCGAGGACAGAAGCCCGAGgtgaccgatcaatccgttgttcttgatttttccttttggttttgattttgcagtgatcgt-ttctgtctctgtctcc--gtcggcgcctggttcttgatcgtgtttgtgcgcgtgtgtgtgcag---------
















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|149100217|gb|EE186279.2|EE186279
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|71306485|gb|DR789390.1|DR789390
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|149009618|gb|EE041571.2|EE041571
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|148965587|gb|EE016422.2|EE016422
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|89761374|gb|DY689412.1|DY689412
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|149014649|gb|EE044313.2|EE044313
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|71330806|gb|DR802200.1|DR802200
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|78075240|gb|DV503674.1|DV503674
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|148954070|gb|EC899469.2|EC899469
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|149070038|gb|EE158438.2|EE158438
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
EST: gi|74241355|gb|DT649269.1|DT649269
EST:     ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAG                         GACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG
genomic: ACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaa ... tcgctcccagGACGAGCCCGTGGAGAGGCCCATGTCCAAGGGCGGCGCCGCCGAGGAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCCCGACGGCGACGTCATCCACTGCGTGCCGGCGCACCTGCAGCCGGCGTTCGACCACCCCAGGCTGAGAGGGCAGGAGCCCGAGgtgagccaaaatcccttgctctacctagcatctagcattagcaagcaccgccgtttcgttctggatctgttccgcggtcgacggagtgtcctgagcaacgtgcgtgtgtgcaattgtgcatcgctcccag

- - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG