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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctaactaataacagttactaattttacatatttcgccgtgggaatgcatgaaagggttttatgttgctgttctgtctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACTGATGCTGAGAAAGCATATTACTTGGAGCACGGGATCACACCACCAAAAT

Basic information

species Zea mays
transcript GRMZM5G801369_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G801369_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 13
----gtaagct-aactaataacagttact-aattttacat-atttcgccgtgggaatgcatgaa----agggttttatgttgctgttctgtctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACTGATGCTGAGAAAGCATATTACTTGGAGCACGGGATCACACCACCAAAAT
    | |  || | |   |   | ||| |  || |||  | ||| |    |      |  |||     |     |  |  |      || | | | |||||| ||||| |||||| | |||||||||||||||||||||| ||||||| ||||||||||||| ||||||||||| |   | ||||||||||| ||||| |
gttcgaagcctcacccccttctaattatttgatattaggtcattccctaatattcgcgtttgagcctcaccacctcttaatatacaactttttttcacagGTGAGAGCTCGCTGTAGAAAAGAATGGGGGATGTTCCAAAAAAGGTTGGCTGATGCTGAGAAGGCATATTACTTAGGAAAAGGGATCACACCGCCAAATT
















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|56461966|gb|CK986264.1|CK986264
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|4621622|gb|AI612455.1|AI612455
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32838018|gb|CD977696.1|CD977696
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|78120790|gb|DV539174.1|DV539174
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32837052|gb|CD976730.1|CD976730
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|6021059|gb|AW065987.1|AW065987
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGNTCCAAACAAGGGTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|6601788|gb|AW256229.1|AW256229
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAANCAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|211502844|gb|FL437375.1|FL437375
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32917091|gb|CF021903.1|CF021903
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|211325390|gb|FL371043.1|FL371043
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|18164577|gb|BM334416.1|BM334416
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|50331568|gb|CO526694.1|CO526694
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32838737|gb|CD978418.1|CD978418
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|32832999|gb|CD972677.1|CD972677
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
EST: gi|12973204|gb|BG268364.1|BG268364
EST:     GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGG                         GTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT
genomic: GGCAAGGCAGAGAATGGAAAAGCACCATGGGAAGGGgtaagctaac ... tctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcgccgtgggaatgcatgaaagggttttatgttgctgttctgtctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACTGATGCTGAGAAAGCATATTACTTGGAGCACGGGATCACACCACCAAAAT
                                        ttctgtct  CT-rich tract
                           ttttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctaactaataacagttactaattttacatatttcgccgtgggaatgcatgaaagggttttatgttgctgttctgtctgttacagGTTAGAGCACGCTGTCGTAAAGAATGGGGGATGTTCCAAACAAGGTTGACTGATGCTGAGAAAGCATATTACTTGGAGCACGGGATCACACCACCAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA