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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgttttattgctagcgtctgttatgtatttaagttacactgtgttgttcttacttcttagtggatgtcttatttgaacag

Basic information

species Zea mays
transcript GRMZM2G086052_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086052_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g40620.1 (Oryza sativa), 5'ss of exon 4
ATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtg-tgttttattgctagcgtctgttatgtatttaagttacactgtgttgttcttacttcttagtggatgtcttatttgaacag
 |||||||||||||||||||||||||||||  |||||| ||| || ||||||||||||||||| ||||| || ||||| |||||||| ||||||||| | ||  ||  ||  |||| || ||| |  | | || || || | |  | |   ||||  |   |  || ||     ||| ||||||
GTGGGCAATGTGCCTCTGGGAGCAAATGGGGCAGCCAGAGAAAGTCAATCTGATTGAGCTTGGTCCAGGGCGCGGAACTCTCTTGGCAGATTTACTTCGTgtaatgcatttctgcttgcatctatcctattttgaactttcccgatttgtgtctt--tgactgatgcat---ccattggaacag

upper sequence: GRMZM2G086052_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT3G28700.1 (Arabidopsis thaliana), 5'ss of exon 4
ATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgttttattgctagcgtctgttatgta-tttaagttacactgtgttgttctta----cttcttagtggatgtctta---tttgaacag---
 ||| |  |||| || |||||||||||||||| ||||| || ||| |||||  ||||||| || ||||| || ||||||||| |||| ||| | ||| | || ||| ||  ||||   || |  |    | ||  |||| |  |   |       |    ||  ||| || ||     |   |||||   |   
TTGGACCGTGTGTCTTTGGGAGCAAATGGGAAGGCCAGAGAGGGTTAATCTTGTTGAGCTAGGTCCAGGTCGGGGAACACTCATGGCCGATCTCCTTCGTgtatgtatttatgctcttgtatccttgacagttctagttccgttccataacctcgatgatctcattactgaatactaaaacctttgacttgtag
















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|71326245|gb|DR799816.1|DR799816
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCTCA-GTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGC-CAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGT
EST: gi|32792113|gb|CD944349.1|CD944349
EST:     TGATTGAGCTTGGCCCAGGACGAAGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGC
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGC
EST: gi|32826797|gb|CD966475.1|CD966475
EST:     TGATTGAGCTTGGCCCAGAACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCCAACTTCACCAAGGCACTGAGCATTA
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTA
EST: gi|71297897|gb|DR784919.1|DR784919
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
EST: gi|93281358|gb|EB673622.1|EB673622
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
EST: gi|78108018|gb|DV526436.1|DV526436
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGGCAAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTT
EST: gi|71313522|gb|DR793329.1|DR793329
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
EST: gi|71297664|gb|DR784782.1|DR784782
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
EST: gi|149097668|gb|EE183570.2|EE183570
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
EST: gi|93281137|gb|EB673401.1|EB673401
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
EST: gi|76293021|gb|DV032589.1|DV032589
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
EST: gi|32824168|gb|CD963890.1|CD963890
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGACACTGAGTATTA
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTA
EST: gi|78090509|gb|DV518883.1|DV518883
EST:     TGATTGAGCTTGGCCCACGACGAGGAACACTCTTGGCTGATTTACTTACG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
EST: gi|71772608|gb|DR970536.1|DR970536
EST:     TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGG                         GGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT
genomic: TGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgtttta ... atttgaacagGGATCGGCCAAGTTTGCTAACTTCACCAAGGCACTGAGCATTAACTTAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTGATTTACTTAGGgtgtgttttattgctagcgtctgttatgtatttaagttacactgtgttgttcttacttcttagtggatgtcttatttgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT