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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcttttaagtctgcagaataaattcttccggaaaatacataacctctttaactatcttggtatttgttaattctttgttttatatgcttaattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCTTCAATTTCAACTCAAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGA

Basic information

species Zea mays
transcript GRMZM2G144716_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144716_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g52720.1 (Oryza sativa), 3'ss of exon 2
ctgcttttaagtctgcagaa----taaattcttccggaaaatacataacctctttaactatcttggtatttgttaattcttt-gttttatatgcttaattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCTTCAATTTCAACTCAAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGA
  ||| | |  |    |||     | |||  |     | | || ||||| || |||  | | |   ||| |  |||||||||  |  || || |  ||||  ||||  |||| |||| |||||| || ||||| || ||||||||||  |  ||||||||||| || |||||||||||||||||||||||||| ||||| |||||
-agctatgacattctaagatgcttttaatcttcatttagagta-ataac-tcatta--tgtttgtctatgtcataattctttcatcctacatacgaaatttgcagCCATTGTGTGGAATTCAGAAGACCTAATCCCACCAAGTGAAAAGTACATCTTCAATTTTAATTCAAAAGATGAGCTGAAAAGGTGGCACTTGTATTCAGA
















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|71429836|gb|DR810886.1|DR810886
EST:     GTCGAGACTGCGAGCTCTGTGACACGCTTCCTTTAACGCCACAGAGAGAG                         CTCTTGTATGGAGTTCAGATGATCTAATTCCCGCCA-GTGAAAGATGTATC
genomic: GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAGgtatgttctt ... taattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCC-GCCAAGTGAAAGATGTATC
EST: gi|12046177|gb|BF728316.1|BF728316
EST:     GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAG                         CTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
genomic: GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAGgtatgttctt ... taattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
EST: gi|78179752|gb|DV550125.1|DV550125
EST:     GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAG                         CTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
genomic: GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAGgtatgttctt ... taattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
EST: gi|6636927|gb|AW261199.1|AW261199
EST:     GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAG                         CTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
genomic: GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAGgtatgttctt ... taattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
EST: gi|78081291|gb|DV509703.1|DV509703
EST:     GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAG                         CTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
genomic: GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAGgtatgttctt ... taattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
EST: gi|6827615|gb|AW331258.1|AW331258
EST:     GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAG                         CTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
genomic: GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAGgtatgttctt ... taattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCT
EST: gi|211180004|gb|FL285245.1|FL285245
EST:     GTCGAGACTGCGAGCTCTGTGGCAGGCTTTCTTTTACGCCACAAAGAGAG                         CTCTTGTATGGAGTTCAGATGATCTAAT
genomic: GTCGAGACTGCGAGCTCTGTGGCAGGCTTCCTTTAACGCCACAAAGAGAGgtatgttctt ... taattgccagCTCTTGTATGGAGTTCAGATGATCTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttaactatcttggtatttgttaattctttgttttatatgcttaattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCTTCAATTTCAACTCAAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGA
                       ttaattctttgtttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcttttaagtctgcagaataaattcttccggaaaatacataacctctttaactatcttggtatttgttaattctttgttttatatgcttaattgccagCTCTTGTATGGAGTTCAGATGATCTAATTCCGCCAAGTGAAAGATGTATCTTCAATTTCAACTCAAAAGATGAGCTGAAAAGGTGGCATTTGTACTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA