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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtacatgcactcaattttgttccaagctactttaccttgtagtccatttagctgcttgtgttgttacagtactaaatgaacaatcttcatggtagttttccttgcataaaatcgtttttatggtatagttaaccttgccccaatgtacttcttctgatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAATGGGCTGACCCTGGTGTTGATGCTTATTCCGCTGCCTCTCTGAGGGCCA

Basic information

species Zea mays
transcript GRMZM2G003509_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 11
gtttgtacatgcactcaattttgttccaagctactttaccttgtagtccatttagctgcttgtgttgttacagtactaaatgaacaatcttcatggtagttttccttgcataaaatcgttttta-tggtatagttaaccttgccccaatgtacttcttctgatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAATGGGCTGACCCTGGTGTTGATGCTTATTCCGCTGCCTCTCTGAGGGCCA
                                   ||  | |    || |||||| ||||    |  ||| || | |   |   | |||||  |     ||  | |||   ||||| |||   | |   | | |||| |||  |  |||||  || || | ||| |||||||||| || ||||||||||||||||||||| ||||||||||||| |||||||||||||| |||||||||||||||||||| ||||| ||| || | ||||
----------------------------------gttgacataggctctatttagttgctcagctaattatag-attgtct---ctatctttgt-----ttcactttgaccaaaattgttccaaatcaaagaattaagctttacaaaatgtcattttttttataatgtagAATGTACCTCCTGCTCTACTTGTGCGATTTCTGAGGGAGCATCGTTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTTCTTTGCGAGCCA

upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 11
gtttgtacatgcactcaattttgttccaagctactttaccttgtagtccatttagctgcttgtgttgttacagtactaaatgaacaatcttcatggtagttttccttgcataaaatcgtttttatggtatagttaaccttgccccaatgtacttcttctgatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAATGGGCTGACCCTGGTGTTGATGCTTATTCCGCTGCCTCTCTGAGGGCCA
    ||||||| |  || || | |      |||    |   | || |    |||      |   |  || || | | ||||      || || |  |  ||  |  | | | ||  | | ||     | |  |  |   |   | | |||||    | ||    |  ||||||| || |||||| | ||||| |||||||||||||||||||| || || ||||||||   ||| |||||||| || || ||||| |  || |  || |
----gtacatg-aaacagttctat---ggactatgacataatataat---attaataatattaataatttcaatgccaaat------tcctctttttgtttcccaattcgtgaag-catcttctaaattttctctataatcatctattgtacaa--tgtgtctctacagAATGTTCCCCCTGCTTTGCTTGTTCGATTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCTGCATGCCTTAAAGCTA

upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 11
gtttgtacatgcactcaattttgttccaagctactttaccttgtagtccatttagctgcttgtgttgttacagtactaaatgaacaatcttcatggtagttttccttgcataaaatcgtttttatggtatagttaaccttgccccaatgtacttcttctgatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAATGGGCTGACCCTGGTGTTGATGCTTATTCCGCTGCCTCTCTGAGGGCCA
                     |     || | | | ||     |    |||   | |  |  | ||  || | |||||  | || | |  || |  |  ||     |     ||     || ||   | |  | |   |   | |  |||||    | |     |  ||||||| || |||||| | ||||| || ||||||||||||||||| || || ||||||||   ||| |||||||| || || || || |  || |  || |
--------------------gtacctgaaacaattctatgggctcaggcataatgttaataatattaatata-tactat-tcaaaatttgtctttttgtttcctaatttgctaagcatcttctaaattttcatcataatcatctct-tgtacaatgttt--ctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA

upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtttgtacatgcactcaat-tttgttccaagc-----tactttaccttgtagtccatttagctgcttgtgt-tgttacagtactaaatgaacaatcttcatggtagttttccttgcataaaatcgtttttatggtatagttaaccttgccccaatgtacttctt--ctgatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAATGGGCTGACCCTGGTGTTGATGCTTATTCCGCTGCCTCTCTGAGGGCCA
           || |  |||  |    ||  | | ||   ||      ||   ||  |||| |    |  | || ||  | | | |  || | | |    |  ||| ||  | | |  | | || |  ||| |||  | ||  |  ||| || |  |  ||  |    |||  ||   |||   || ||||||| || |||||| ||||||| |||||  |||| || || || ||||| |||||||||  |||||||||||||||||| ||||| | ||| |  || |
gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggat-gtccaacttctgttttatctctcaatgccaccccacaaatattatttgaa--tcttctgggttaacatcactatt--gaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA

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|211416749|gb|FL321414.1|FL321414
EST:     CTGCCATGGGGGGCGGCATCATGTGCGCAAAAGCGTCAATGCTACTGCAG                         AATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAA
genomic: CTGCCATGGGGGGCGGCATCATGTGCGCAAAAGCGTCAATGCTACTGCAGgtttgtacat ... gatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAA
EST: gi|211510674|gb|FL361528.1|FL361528
EST:     CTGCCATGGGGGGCGGCATCATGTGCGCAAAAGCGTCAATGCTACTGCAG                         AATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAA
genomic: CTGCCATGGGGGGCGGCATCATGTGCGCAAAAGCGTCAATGCTACTGCAGgtttgtacat ... gatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAA
EST: gi|211126699|gb|FL314385.1|FL314385
EST:     CTGCCATGGGGGGCGGCATCATGTGCGCAAAAGCGTCAATGCTACTGCAG                         AATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAA
genomic: CTGCCATGGGGGGCGGCATCATGTGCGCAAAAGCGTCAATGCTACTGCAGgtttgtacat ... gatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgtttttatggtatagttaaccttgccccaatgtacttcttctgatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAATGGGCTGACCCTGGTGTTGATGCTTATTCCGCTGCCTCTCTGAGGGCCA
                                         ttctgat  putative branch site (score: 3)
                                     cttcttctg  CT-rich tract
             tatagttaa  TA-rich tract