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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttcctcatcttatattattattaccgaggaacaatgctttgcattttatacctagaatagctcttactgacatgttgaaccacttgaagcctcctagtaggcttaattccatgtgtatcctatcacctcattaagttggtgctgacttgtttgtgttattgccag

Basic information

species Zea mays
transcript GRMZM2G459642_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G459642_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g74310.5 (Oryza sativa), 5'ss of exon 6
AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgtt-attcttcctcatcttatattattattaccgaggaac---------------aatgctttgcattt-------tatacctagaatagctcttactgacatgttgaaccacttgaagcctcctagtaggcttaattccatgtgtatcctatcacctcattaagttggtgctgac---ttgtttgtgttattgccag
|||||||||||||| || ||||| |  |||||||||||||||||||| |||||||||||||||||||||||  |  ||   |  || ||| | |||||    | | ||                |||||  | ||| |       | || ||||| ||| |  |  |  || |        ||| |||  || ||| ||| || ||| ||||  ||||  ||  |   |||| || ||| |||||   || |||   || |||||||
AGAATGATGACAGAAGAGCCAGATACCTACCAACGGATGCTTCAAAGTCTCATCTCAAAAGCTCAACAGgtggagcctcttttttcctatctcattatgggggtgaaatttgaagtattacatgaatgccatccatatgcatcggtttatctagattagtttctggtttcacgccaggt-gcttcaagtgtcgtaggaggtttcatttcatgcatatctgatatctcaattatgtcggtactgacatgttatttacattgttgccag
















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|60346719|gb|DN213692.1|DN213692
EST:     CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|60399844|gb|DN232654.1|DN232654
EST:     CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|60353564|gb|DN220537.1|DN220537
EST:     AAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: AAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|211383655|gb|FL455017.1|FL455017
EST:     AGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: AGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|33091264|gb|CF051258.1|CF051258
EST:     CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|60344784|gb|DN211757.1|DN211757
EST:     CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
EST: gi|6056553|gb|AW090943.1|AW090943
EST:     CAGAGATATACCAACGGATGCTTNAAAGCCTCATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTT
genomic: CAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTT
EST: gi|60401545|gb|DN234352.1|DN234352
EST:     ATCTCAAAAGCTCAACAG                         TGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA
genomic: ATCTCAAAAGCTCAACAGgttattcttc ... ttattgccagTGTAACAATGAGAAACTTCTGGAGAACCCATACCTTCAGATGCGTGGGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAGgttattcttcctcatcttatattattattaccgaggaacaatgctttgcattttatacctagaatagctcttactgacatgttgaaccacttgaagcctcctagtaggcttaattccatgtgtatcctatcacctcattaagttggtgctgacttgtttgtgttattgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA