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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGATGGGTCACCTGTGTCAATTTTTTCTCTGTCAGGGAGCAACCCTCAGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACGgtaagctaacaacttcagtcactgggtttctgattaccaatattcaatagtgctgtaccttttagacttgaggagcagtgtacaaagccttctttcagaa...

Basic information

species Zea mays
transcript GRMZM2G098078_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098078_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 2
GATGATGGGTCACCTGTGTCAATTTTTTCTCTGTCAGGGAGCAACCCTCAGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACGgtaagctaacaacttcagtcactgggtttctgattaccaatattcaatagtgctgtaccttttagacttgaggagcagtgtacaaagccttctttcagaa------
||||||||||| || |||||||| |||||||||||||||||||| ||||||||||| ||| |||||||||| || ||||||||||||||||||||||| ||||| ||  ||  |   ||  |   | | ||      ||| |  | | || ||| |  | |   | || |  ||  | | |   || ||    | | |       
GATGATGGGTCGCCCGTGTCAATCTTTTCTCTGTCAGGGAGCAATCCTCAGGACAGGCACTTGGTTGCTGGTCGGAATGGTGTTAAGAGATTACGAACAgtaagttactaatgttgatc-ttaaatatttg-----taatgtctacttgtactgcaagtgtcttattttaacagatgagaatggagtctatggtgatatactatt
















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|211424859|gb|FL220407.1|FL220407
EST:     AGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACG                         GTGCGGCATCCAAATATCTTATCCTTTTTACACAGTACTGAAGCAGAAGTT
genomic: AGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACGgtaagctaac ... gttactgcagGTGCGGCATCCAAATATCTTATCCTTTTTACACAGTACTGAAGCAGAAGTT
EST: gi|211424858|gb|FL220406.1|FL220406
EST:     AGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACG                         GTGCGGCATCCAAATATCTTATCCTTTTTACACAGTACTGAAGCAGAAGTT
genomic: AGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACGgtaagctaac ... gttactgcagGTGCGGCATCCAAATATCTTATCCTTTTTACACAGTACTGAAGCAGAAGTT
EST: gi|76289771|gb|DV029339.1|DV029339
EST:     AGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACG                         GTGCGGCATCCAAATATCTTATCCTTTTTACACAGTACTGAAGCAGAAGTT
genomic: AGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACGgtaagctaac ... gttactgcagGTGCGGCATCCAAATATCTTATCCTTTTTACACAGTACTGAAGCAGAAGTT
EST: gi|211352110|gb|FL449964.1|FL449964
EST:     AGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACG                         GTGCGGCATCCAAATATCTTATCCTTTTTACACAGTACTGAAGCAGAAGTT
genomic: AGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACGgtaagctaac ... gttactgcagGTGCGGCATCCAAATATCTTATCCTTTTTACACAGTACTGAAGCAGAAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGATGGGTCACCTGTGTCAATTTTTTCTCTGTCAGGGAGCAACCCTCAGGACAGACACATGGTTGCTGGCCGTAATGGTGTTAAGAGATTACGAACGgtaagctaacaacttcagtcactgggtttctgattaccaatattcaatagtgctgtaccttttagacttgaggagcagtgtacaaagccttctttcagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA