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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtcattagagcacatcattgatcctcctagtatctgttctttgctaactacgcagtataaccttctcattctcatgtatttattatttgtcaccccttgtactgataccag

Basic information

species Zea mays
transcript GRMZM2G073571_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073571_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 5'ss of exon 9
TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtcattagagcacatcattgatcctcctagtatctgttctttgctaactacgcagtataaccttctcattctcatgtatttattatttgtcaccccttgtactgataccag
||||||||| ||||||||||||||| ||||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||||||| ||||||||| || | | || | |||      | | | || |  ||    |||   || |  |   | | |    |||| |||||    ||  |||| || || |||| |      || ||||||||||||
TGAATTGCCGGAATTCCTTGGTGGCGCTTGTACCTGTCCTGAATATGGAGGGTGTCTTAAAGCTGAAAAAGGACCATGGAAGGACCAAAACATACTCAATgtacgtttgatttc--ttccttactgtttgtc----tattcattatcagtgcattgctttctatacccttcc---tcatatgttttaataatttttt-----ttatactgataccag
















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|15177587|gb|BI398526.1|BI398526
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15323596|gb|BI478854.1|BI478854
EST:     GCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15188204|gb|BI417181.1|BI417181
EST:     TTAAGGCTGAAAAGGGACCGTGGAAGGACCCAGGCATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: TTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|16137338|gb|BI894203.1|BI894203
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTTA-TTC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAAC-TATTTC
EST: gi|16137339|gb|BI894204.1|BI894204
EST:     GGCTG-AAAGGGACCGTGG-AGGACCCAAACATACTTAATG                         ATAGTCC-AAGTGGTGGGGTTCATTGTGCTCGTCAAA-TGTAACTATTT-
genomic: GGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAA-Ggcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTC
EST: gi|32832349|gb|CD972027.1|CD972027
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|32847771|gb|CD987452.1|CD987452
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|3172014|gb|AJ006545.1|AJ006545
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15177586|gb|BI398525.1|BI398525
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|8383108|gb|BE055991.1|BE055991
EST:     GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
genomic: GTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC
EST: gi|15323597|gb|BI478855.1|BI478855
EST:     TTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAG                         ATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTAATTCC
genomic: TTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtca ... ctgataccagATAGTCCAAAGTGGTGGGGTTCATTGTGCTCGTCAAATTGTAACTATTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATTGCCAGAATTCCTTGGTGGCACTTGTACCTGTCCTGAATACGGAGGTTGCCTTAAGGCTGAAAAGGGACCGTGGAAGGACCCAAACATACTTAAGgcatgtgtcattagagcacatcattgatcctcctagtatctgttctttgctaactacgcagtataaccttctcattctcatgtatttattatttgtcaccccttgtactgataccag

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