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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGTTGAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagccatcttgcatgaatttcacctctctactatctctctccgttaaggcatgaacgatccacttaccttgcattcatctctgaacag

Basic information

species Zea mays
transcript GRMZM2G375904_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g43570.3 (Oryza sativa), 5'ss of exon 13
CAGAGTTGAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagccatcttgc-atgaatttcacctctctactatctctctccgttaaggcatgaacgatccacttaccttgcattcatctctgaa-cag
| ||||||||||| |||||||||||  ||||||| ||||| ||||||||| | ||||||| |||||  | ||   |   |||    |  | ||| | |     |||||      |  | |||    ||| ||||| || |||  | || |||
CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTGgtattgagcactattattacctattggttccttatac-accatgtaccgttt-----ttcatgatatgtttaacttgcttttatccttaaaacag
















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|5895617|gb|AW036863.1|AW036863
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|28187719|gb|CB179329.1|CB179329
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|5901099|gb|AW042199.1|AW042199
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|33285627|gb|CF075422.1|CF075422
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACNAAGAGGAGCCTGTTCA-GGGA
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGA
EST: gi|211195854|gb|FL001022.1|FL001022
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|32934179|gb|CF038991.1|CF038991
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGGCCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|149049839|gb|EE048526.2|EE048526
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
EST: gi|32870336|gb|CF010018.1|CF010018
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTAT
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTAT
EST: gi|5597186|gb|AI891179.1|AI891179
EST:     GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTG                         AGAGGATGGACGGAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC
genomic: GAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagcc ... ctctgaacagAGAGGATGGACGAAGAGGAGCCTGTTCAAGGGAGTTTCTTAAGTATGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGTTGAAGAAAAAGAGTTCCAAACCAAAGCGACCAACCATCAAGACAATGTTTGgtaatgagccatcttgcatgaatttcacctctctactatctctctccgttaaggcatgaacgatccacttaccttgcattcatctctgaacag

- - - - AAGAAA