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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcatcgccccgtccaattcctgattggttgattgtttactgtttggttgctgattttggtgtcatttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTGACGGTGGTGGCGATGCCGATAGCGTGACCTCCATGTCCAGTGGGCTGTC

Basic information

species Zea mays
transcript GRMZM2G057412_T04
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|89759048|gb|DY687994.1|DY687994
EST:     TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGA                         GTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
genomic: TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGAgtgcgcatcg ... tttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
EST: gi|50339208|gb|CO534334.1|CO534334
EST:     TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGA                         GTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
genomic: TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGAgtgcgcatcg ... tttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
EST: gi|74240131|gb|DT648045.1|DT648045
EST:     TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGA                         GTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
genomic: TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGAgtgcgcatcg ... tttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
EST: gi|101398967|gb|EB821356.1|EB821356
EST:     TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGA                         GTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
genomic: TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGAgtgcgcatcg ... tttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
EST: gi|211098028|gb|FL078453.1|FL078453
EST:     TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGA                         GTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
genomic: TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGAgtgcgcatcg ... tttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
EST: gi|89759388|gb|DY688240.1|DY688240
EST:     TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGA                         GTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
genomic: TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGAgtgcgcatcg ... tttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
EST: gi|211386246|gb|FL227578.1|FL227578
EST:     TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGA                         GTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
genomic: TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGAgtgcgcatcg ... tttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
EST: gi|93281098|gb|EB673362.1|EB673362
EST:     TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGA                         GTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG
genomic: TTCTTGGCCTCTTCGCTTCCTGGACCGCCCAGACGTCTCCATGGGCAAGAgtgcgcatcg ... tttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattggttgattgtttactgtttggttgctgattttggtgtcatttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTGACGGTGGTGGCGATGCCGATAGCGTGACCTCCATGTCCAGTGGGCTGTC
                            tgctgat  putative branch site (score: 3)
                                             tttgtctt  putative PPT
           attgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcatcgccccgtccaattcctgattggttgattgtttactgtttggttgctgattttggtgtcatttgtcttagGTAAGAGGAACAAGGGCGGTCGAGGTGGTGGTGGTGCCGATGACAAGCTTGACGGTGGTGGCGATGCCGATAGCGTGACCTCCATGTCCAGTGGGCTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG