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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctgctctgtgctggattcaacacccaccgaatcctgttacgacttaccacaccacaccgatgcaatcggtatcttcctttttcatttcaactgatggtccaataacaaccaccaaaccctgcag

Basic information

species Zea mays
transcript GRMZM2G085747_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os10g35960.1 (Oryza sativa), 5'ss of exon 17
CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctgctctgtgctggattcaacacccaccgaatcctgttacgacttaccacaccacaccgatgcaatcggtatcttcctttttcatttcaactgatggtccaataacaaccaccaaaccctgcag
||| || ||||||||||||||||| |||||||||||||| |||||||| || ||  |||| ||||  |||||  ||  | |    | |     |||  | |  ||| || |    |  | |||| |   || ||| |   ||    ||||| |   |||||  ||    | || | ||   |            
CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAGgttagctct--tccatccaacctgcg----ccattgcagactgataggcagcatgataccata---atccaacc---attccacttttgctaatcaac--ataccaccatgaaaaatgcag----------
















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|211281985|gb|FL018038.1|FL018038
EST:     AGACGACGAAATTCGAAAAGGAATCCTCCTCTCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: AGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|4647288|gb|AI622363.1|AI622363
EST:     ATCACAGNCGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCNCCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|32933889|gb|CF038701.1|CF038701
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|71758667|gb|DR956604.1|DR956604
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|211281986|gb|FL018039.1|FL018039
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|86470645|gb|DY237015.1|DY237015
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|74232917|gb|DT640831.1|DT640831
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|4730607|gb|AI649773.1|AI649773
EST:     GACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCCCCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: GACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|76919652|gb|DV167818.1|DV167818
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|50334197|gb|CO529323.1|CO529323
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|113701975|gb|EE679479.1|EE679479
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|40303330|gb|CK347717.1|CK347717
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|211050465|gb|FL475129.1|FL475129
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|213169886|gb|FM184059.1|FM184059
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|211281987|gb|FL018040.1|FL018040
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|4647287|gb|AI622362.1|AI622362
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCNCCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|74232916|gb|DT640830.1|DT640830
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|74238357|gb|DT646271.1|DT646271
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|211326815|gb|FL454067.1|FL454067
EST:     ATCMCAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCMCCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|26456270|gb|CA827853.1|CA827853
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCG
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCG
EST: gi|78544875|gb|DV622373.1|DV622373
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|30032196|gb|CB834047.1|CB834047
EST:     ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
EST: gi|12971899|gb|BG267713.1|BG267713
EST:     ATCACAGACGGCGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG                         TATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT
genomic: ATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctg ... aaccctgcagTATTAGGCACATCACCGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAGgtgggctctgctctgtgctggattcaacacccaccgaatcctgttacgacttaccacaccacaccgatgcaatcggtatcttcctttttcatttcaactgatggtccaataacaaccaccaaaccctgcag

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