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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctggttgaaacagacatttacacttgcatatagtcaaatgcatccaggccaacctagatttggatccaaatttatcgaattggcgatctctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGGCTCAGAGGAGGTAGACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGA

Basic information

species Zea mays
transcript GRMZM2G112782_T02
intron # 1
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|148970852|gb|EE021628.2|EE021628
EST:     AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTT                         GATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
genomic: AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTTgtgagtgcct ... ctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
EST: gi|76287560|gb|DV027128.1|DV027128
EST:     AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTT                         GATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
genomic: AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTTgtgagtgcct ... ctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
EST: gi|149070489|gb|EE158892.2|EE158892
EST:     AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTT                         GATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
genomic: AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTTgtgagtgcct ... ctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
EST: gi|211046462|gb|FL097856.1|FL097856
EST:     AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTT                         GATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
genomic: AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTTgtgagtgcct ... ctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
EST: gi|148931764|gb|EC875027.2|EC875027
EST:     AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTT                         GATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
genomic: AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTTgtgagtgcct ... ctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
EST: gi|148932521|gb|EC876312.2|EC876312
EST:     AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTT                         GATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
genomic: AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTTgtgagtgcct ... ctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
EST: gi|93016784|gb|EB642304.1|EB642304
EST:     AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTT                         GATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
genomic: AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTTgtgagtgcct ... ctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
EST: gi|211046465|gb|FL097859.1|FL097859
EST:     AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTT                         GATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG
genomic: AAGGACGGGTTCTTCCAGGCGGCCGAGGAGGTGCAGGAGTCCGCGGACTTgtgagtgcct ... ctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggccaacctagatttggatccaaatttatcgaattggcgatctctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGGCTCAGAGGAGGTAGACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGA
                                          tctctccttgt  CT-rich tract
                       aaatttatcgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctggttgaaacagacatttacacttgcatatagtcaaatgcatccaggccaacctagatttggatccaaatttatcgaattggcgatctctccttgtagGATGGAATCAGTCTATAGAACTTGGATGCGTGAGCGTAGTAATGGATCTGGCTCAGAGGAGGTAGACGATTTGCAAAGGGAGCTTCAGACAGCTTTAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT