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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacccgtccgtccgtccatccatctatccatccatccagcagcaggaacaaatttaccacaagacgtctggaaatcaccggccacaaagacgtctggagatctgcatctgctaacaacgttttctctccctttttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGGTACATGACCTTCGACGAGCTCTACCTCTACTGCTACTACGTCGCCGGCA

Basic information

species Zea mays
transcript GRMZM2G149317_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149317_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
gtaaacccgtccgtccgtccatccatctatccatccatccagcagcaggaacaaatttaccacaagacgtctggaaatcaccggccacaaagacgtctggagatctgcatctgctaacaacgttttctct-------ccctttttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGGTACATGACCTTCGACGAGCTCTACCTCTACTGCTACTACGTCGCCGGCA
                     | || | | | |   | | | | | |  | ||   |      |   | | |  || | |   |  ||| ||     ||| ||   |||| ||         | | | |         |  |||| |   ||||| |||||||||||| |  ||||||||||||| ||||||||||| || ||||| | || ||| || |||||||||||||||||||||||||| || ||||
--------------------gtacagccaacaaaaaagcta-ctgtaaaagcaggata--tgaagtgcttttaaaagttattagt-acacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA

upper sequence: GRMZM2G149317_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 3
gtaaacccgtccgtccgtccatccatctatccatccatccagcagcaggaacaaatttaccacaagacgtctggaaatcaccggccacaaagacgtctggagatctgcatctgctaacaacgttttctctccctttttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGGTACATGACCTTCGACGAGCTCTACCTCTACTGCTACTACGTCGCCGGCA
                                       || |      ||    |  | |  |    |  | ||  |||||   |      | ||    | | |||   |   |  ||  |  || |||     ||||    ||||| ||||| |||||| || |||| |||||| |||||||| | ||||| || ||||  | ||| || ||||||||||| ||||||||||| || || || |
--------------------------------------gcacctatgcaaattggtc-atcttatacagaatagatttcacct-tcttttttatgtgctaaaa-ctgatccaaatggcattgcattgtct-----ttttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGATACAATAACTTTGATGAGCTCTACCTTTACTGCTACTATGTTGCTGGGA

upper sequence: GRMZM2G149317_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ16279 (Selaginella moellendorffii), 3'ss of exon 3
gtaaacccgtccgtccgtccatccatctatccatccatccagcagcaggaacaaatttaccacaagacgtctggaaatcaccggccacaaagacgtctggagatctgcatctgctaacaacgttttctctccctttttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGGTACATGACCTTCGACGAGCTCTACCTCTACTGCTACTACGTCGCCGGCA
                                                                               |      | | |    ||| | |      || |||| |  |    |||  ||   |  ||    |||||||||   |||||| |  |||| ||| | ||||| |||   |||||||||||||  |  || |||||||| ||||| || |||||||||||||||||||
-----------------------------------------------------------------------------gtattctaaagacatttctcttgcggatattatatgctgatca----ttccttcgaatcgttcatgcagCCGTTCCGGGACATGATAGAAGGCATGCGACTGGATCTGGTAAAGTCGAGGTACAAAAATTTTGACGAGCTTTACCTGTATTGCTACTACGTCGCCGGCA

upper sequence: GRMZM2G149317_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ17751 (Selaginella moellendorffii), 3'ss of exon 3
gtaaacccgtccgtccgtccatccatctatccatccatccagcagcaggaacaaatttaccacaagacgtctggaaatcaccggccacaaagacgtctggagatctgcatctgctaacaacgttttctctccctttttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGGTACATGACCTTCGACGAGCTCTACCTCTACTGCTACTACGTCGCCGGCA
                                                                         | | ||    | |||     |   ||  ||| |  || |||| |  |    |||  ||   |  ||    |||||||||   |||||| |  |||| ||| | ||||| |||   |||||||||||||  |  || |||||||| ||||| || |||||||||||||||||||
-------------------------------------------------------------------------gtattctaaagacac---ttctcttgcggatat-tatatgctgatca----ttccttcgaatcgttcatgcagCCGTTCCGGGACATGATAGAAGGCATGCGACTGGATCTGGTAAAGTCGAGGTACAAAAATTTTGACGAGCTTTACCTGTATTGCTACTACGTCGCCGGCA

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|1531735|gb|AA051885.1|AA051885
EST:     ACGACGCCGCGCTCTCGGACACTGTGTCCAAGTTCCCCGTCGATATCCAG                         CCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGG
genomic: ACGACGCCGCGCTCTCGGACACTGTGTCCAAGTTCCCCGTCGATATCCAGgtaaacccgt ... ttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgtctggagatctgcatctgctaacaacgttttctctccctttttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGGTACATGACCTTCGACGAGCTCTACCTCTACTGCTACTACGTCGCCGGCA
                    tgctaac  putative branch site (score: 1)
                          caacgttttctctccc  CT-rich tract
                                          ttttttt  TA-rich tract