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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgacagtttattatcggaaagcagtcacagctaaacatttcatctgcataggctacctcttgagtgataggtggctttgctttttgaaccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGTGGCAAGGTGATTGCTATCAGTGACGTCACAGGCGCCGTCAAAAACGTCG

Basic information

species Zea mays
transcript GRMZM2G178415_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 6
--------cttgacagtttattatcggaaagcagtcacagctaaacatttcatctgcataggctacctcttgagtgataggtggctttgctttttgaaccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGTGGCAAGGTGATTGCTATCAGTGACGTCACAGGCGCCGTCAAAAACGTCG
         |       ||    |   |||  ||  | |||| |||||||   ||||| |||||   ||     |||    |    ||||  |       |||| |||||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||||||||||||||| |||||||| ||||| || || ||||| |||  | 
ctttatgtttacttgagttgaccttacaaattaggga-agctgaacatttttcctgcaaaggctgtgtcacagatgaccaatta--ttgccctgg-----cttttcagGGATTTGGTAATGTTGGATCCTGGGCTGCTCAGCTGATCAGTGAAGCTGGTGGCAAGGTGATTGCCATCAGTGATGTCACTGGAGCTGTCAAGAACAGCA
















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|148940231|gb|EC885000.2|EC885000
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|71426412|gb|DR807462.1|DR807462
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|148966781|gb|EE017869.2|EE017869
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCCGTAACGTTGG
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGG
EST: gi|148934217|gb|EC878238.2|EC878238
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|78089717|gb|DV518091.1|DV518091
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|60354014|gb|DN220987.1|DN220987
EST:     TGCTTGCAGAGCACGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|87152935|gb|DY397724.1|DY397724
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTC
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTC
EST: gi|91867926|gb|EB399854.1|EB399854
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|78092010|gb|DV520384.1|DV520384
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|19436213|gb|BM952623.1|BM952623
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|149101283|gb|EE187396.2|EE187396
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|148981458|gb|EE027657.2|EE027657
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGGTCCTGGGCAGCTCAGCTGATAAGTGAAAGC-GG
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAA-GCCGG
EST: gi|71323470|gb|DR798386.1|DR798386
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCCGG
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCC-GG
EST: gi|149096793|gb|EE182577.2|EE182577
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|211300259|gb|FL012334.1|FL012334
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|13125987|gb|BG316662.1|BG316662
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|87156586|gb|DY401375.1|DY401375
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|71328974|gb|DR801177.1|DR801177
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACG
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACG
EST: gi|149110227|gb|EE190296.2|EE190296
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|148994453|gb|EE034100.2|EE034100
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACGG                         GGATTCGGTAACGTTGGTTCCTGGGCA
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCA
EST: gi|19351121|gb|BM895653.1|BM895653
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|26559718|gb|CA831953.1|CA831953
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
EST: gi|60357158|gb|DN224131.1|DN224131
EST:     TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAG                         GGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT
genomic: TGCTTGCAGAGCATGGCAAAGGCATTGCAGGCCAGCGTTTCGTCATACAGgtagatggtg ... ccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcataggctacctcttgagtgataggtggctttgctttttgaaccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGTGGCAAGGTGATTGCTATCAGTGACGTCACAGGCGCCGTCAAAAACGTCG
                                             ccctttgc  CT-rich tract
                                     tttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgacagtttattatcggaaagcagtcacagctaaacatttcatctgcataggctacctcttgagtgataggtggctttgctttttgaaccctttgcagGGATTCGGTAACGTTGGTTCCTGGGCAGCTCAGCTGATAAGTGAAGCCGGTGGCAAGGTGATTGCTATCAGTGACGTCACAGGCGCCGTCAAAAACGTCG

- - - - - - - - - - - gcagtca
- - - - - - - - - - - - - - - - - - - - - catctgc