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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAACGAAGCGATCGGGGCAGACGGGATCATCAGCACGGAGTGCAAGGAAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagcgctagctagctagagtttctgcgtttcatacctctgtttagctagctctgaactccagttaatctgcccttgacactgcatgcag

Basic information

species Zea mays
transcript GRMZM2G123029_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123029_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g04630.3 (Oryza sativa), 5'ss of exon 7
GGTGAACGAAGCGATCGGGGCAGACGGGATCATCAGCACGGAGTGCAAGGAAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagcgctagctagctagagtttctgcgtttcat----acctctgtttag--ctagctctgaactccagttaatctgcccttgacactgcatgcag----------------------------------
||||||| | || || ||||| || || |||||||||||||| ||||| ||||| || ||| |||| ||||||||||||||| || ||||||| |||||||| |||||  |||   | |||  | |||      |||      ||||  |  | |  |   | |||        ||    ||     |  ||| | || |                                   
GGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGCACGGAATGCAAAGAAGTGGTTAGCGAGTATGGAGAGATGATCCTCAACTTGCTCATAGCACAGgtttgctaa-gctcttt-gctgtattttacagacttctgtgcgacctaagcatggaacagacgctgtgtcgtgattgtgttgtgtgagttact-cttgaactctagtaatgtgctgatgttttgtgtctgagcag
















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|149100422|gb|EE186497.2|EE186497
EST:     AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|149078277|gb|EE167036.2|EE167036
EST:     ATGCTCATGGCACAG                         ACGGATCCACAGAGGGGGTGCAGCCAGGTTGGTCTGTGGGTGTTTGATGGC
genomic: ATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|6827002|gb|AW330645.1|AW330645
EST:     AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|110520668|gb|EE024852.1|EE024852
EST:     AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32844397|gb|CD984078.1|CD984078
EST:     TACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: TACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32923207|gb|CF028019.1|CF028019
EST:     ACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: ACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32844224|gb|CD983905.1|CD983905
EST:     ACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGCGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: ACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32845458|gb|CD985139.1|CD985139
EST:     ACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: ACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32844408|gb|CD984089.1|CD984089
EST:     ACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: ACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|148987680|gb|EE031561.2|EE031561
EST:     AAGTTTTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAACGAAGCGATCGGGGCAGACGGGATCATCAGCACGGAGTGCAAGGAAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagcgctagctagctagagtttctgcgtttcatacctctgtttagctagctctgaactccagttaatctgcccttgacactgcatgcag

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