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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattaaaacatcatcatttttagtttatagggcatttttataaggcaccttgttggagatgctcttactaattaaattaaattgttaatgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG

Basic information

species Zea mays
transcript GRMZM5G871861_T03
intron # 2
splice site 3'
intron type U2

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|211149058|gb|FK958475.1|FK958475
EST:     GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAG                         ATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
genomic: GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAGgtgtgatgat ... tgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
EST: gi|22546278|gb|BU098589.1|BU098589
EST:     GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAG                         ATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
genomic: GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAGgtgtgatgat ... tgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
EST: gi|149004383|gb|EE039059.2|EE039059
EST:     GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAG                         ATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
genomic: GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAGgtgtgatgat ... tgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
EST: gi|13557642|gb|BG548998.1|BG548998
EST:     GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAG                         ATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
genomic: GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAGgtgtgatgat ... tgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
EST: gi|78113561|gb|DV531952.1|DV531952
EST:     GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAG                         ATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
genomic: GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAGgtgtgatgat ... tgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
EST: gi|71449411|gb|DR830461.1|DR830461
EST:     GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAG                         ATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
genomic: GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAGgtgtgatgat ... tgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
EST: gi|149001459|gb|EE038760.2|EE038760
EST:     GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAG                         ATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT
genomic: GAGATCCAGGCAGTGCTCGTGTTCCTGGTGCTCTTCGTAGTGAAGgtgtgatgat ... tgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaccttgttggagatgctcttactaattaaattaaattgttaatgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG
                   tcttactaattaaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaattaaaacatcatcatttttagtttatagggcatttttataaggcaccttgttggagatgctcttactaattaaattaaattgttaatgctcagcagATTGTGAAAGAGGAAACCTGGGAAGCAGTAATTGCTGACTCGTTGCTTTATGCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - aacatca
- - - - - - - - - - - - - - - - - - - - - - - gcacctt