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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTTCCATGGGTTTTGCAACATTTGGTGTCTTCCTTCTTGCAAAGCGTGCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAGgtgcctaactccttacatcacttccttttagaacattctaatgaaatgtagtaacattctttaatagggtgtttgttttgagggatgggtaatgggttag...

Basic information

species Zea mays
transcript GRMZM2G020574_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020574_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g45350.2 (Oryza sativa), 5'ss of exon 8
TTGCTTCCATGGGTTTTGCAACATTTGGTGTCTTCCTTCTTGCAAAGCGTGCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAGgtgc---ctaactccttacatcacttccttttagaacattctaatgaaatgtagtaacattctttaatagggtgtttgttttgagggatgggtaatgggttag
||||||||||||| |||||| ||||||||||||| |||||||||||||||||||||||||||||||| ||||||| ||| || |||||| | || || |||||    |||||     || | | ||   |||||| |   |   | |     | | |||||||| | | |  || |   ||||   ||   |    |  | | 
TTGCTTCCATGGGATTTGCAGCATTTGGTGTCTTTCTTCTTGCAAAGCGTGCACTACAGCATTTTCTCGAAAGAAAACGACGACATGAATTACAGAAGAGgtgtgtgctaaccaaccac-ttatttggatttaga-cggacatgttactcccatttacattcttcagtggtttgctcactttgctagacatggtcagaatga-
















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|78091037|gb|DV519411.1|DV519411
EST:     GCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAG                         GGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
genomic: GCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAGgtgcctaact ... actcatatagGGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
EST: gi|71762996|gb|DR960933.1|DR960933
EST:     GCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAG                         GGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
genomic: GCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAGgtgcctaact ... actcatatagGGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
EST: gi|87152514|gb|DY397303.1|DY397303
EST:     ACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAG                         GGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
genomic: ACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAGgtgcctaact ... actcatatagGGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
EST: gi|24764606|gb|CA399770.1|CA399770
EST:     AAGACGGCGGCATGAACTGCAAAAAAG                         GGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
genomic: AAGACGGCGGCATGAACTGCAAAAAAGgtgcctaact ... actcatatagGGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
EST: gi|71440171|gb|DR821221.1|DR821221
EST:     GCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAG                         GGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
genomic: GCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAGgtgcctaact ... actcatatagGGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
EST: gi|18659370|gb|BM500302.1|BM500302
EST:     GCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAG                         GGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
genomic: GCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAGgtgcctaact ... actcatatagGGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
EST: gi|71759763|gb|DR957700.1|DR957700
EST:     AAGAAGACGGGGGCATGAACTGCAAAAAAG                         GGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG
genomic: AAGAAGACGGCGGCATGAACTGCAAAAAAGgtgcctaact ... actcatatagGGTTCTTAATGCAGCAGCACAAAGGCAAGCTAGAGAAGCTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTTCCATGGGTTTTGCAACATTTGGTGTCTTCCTTCTTGCAAAGCGTGCACTACAGCATTTTCTAGAAAGAAGACGGCGGCATGAACTGCAAAAAAGgtgcctaactccttacatcacttccttttagaacattctaatgaaatgtagtaacattctttaatagggtgtttgttttgagggatgggtaatgggttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG