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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagatggtcttgaacttttgttcaatgttgccctctcttttatatggttttggtataatactgtaatatgaaacaaagaatctgatttgtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC

Basic information

species Zea mays
transcript GRMZM2G109039_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109039_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G13340.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------ttgagatggtcttgaacttttgttcaatgttgccctctcttttatatggttttggtataatactgtaa-----tatgaaacaaagaatctgatttgtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC
                                                       |     || |        ||| ||   | | ||    |  |  | ||    || || || | ||  ||      ||   |  |||||| |   |||       |||| |||||||||||||||||||| || ||||||||| | || ||  | ||  |||      ||   || |  ||  |  | |    ||   |   |||| 
gttttttttttttaatattgagagctcactaacttggactagttgatagtctttctctttctgattggatttatttattgtgtttggcgtgattgtggacataacatttgtctactgctaaaaacctccatctgatcaagaatttttattggtgtcatagCTGAGAAATTTGGTATGGGCAACTTCTAAGCACGACGTGTATCTTATGTCAAATTTTCTGGTTACACATTATTCTTCTCTAACGTCTGGAAAGCATGAAG
















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|58029875|gb|CX725302.1|CX725302
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGGCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|5510853|gb|AI857237.1|AI857237
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20301188|gb|BQ164131.1|BQ164131
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20301181|gb|BQ164124.1|BQ164124
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20300911|gb|BQ163854.1|BQ163854
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20301275|gb|BQ164218.1|BQ164218
EST:     AGTTTAGACGAAATACTAGATCGG-TAAATCAACTATTCTACATTTTCAG                         CTTAGAAA-TTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|20300918|gb|BQ163861.1|BQ163861
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
EST: gi|26456084|gb|CA827667.1|CA827667
EST:     AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG                         CTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT
genomic: AGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAGgtgagttaac ... gtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttttggtataatactgtaatatgaaacaaagaatctgatttgtgcctgcagCTTAGAAATTTGGTATGGGCAACGTCCAAGCACGACATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAAC
                                    atctgat  putative branch site (score: 4)
          tataatactgtaatat  TA-rich tract