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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattttcgtacagtgtaccatcctttttttttccagtgcatatgcattttctgctgtctaaaaactcatgcaaattgctggtttctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCATGACATCCAGAGCACAACTTCATGACTTGGAACATGGTCACTATGAGAT

Basic information

species Zea mays
transcript GRMZM2G083475_T01
intron # 19
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|211192660|gb|FL425751.1|FL425751
EST:     ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTKGGACCATGGTATTCGSGAGAATGTGAAATCCATCGTCA
genomic: ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
EST: gi|19351673|gb|BM896205.1|BM896205
EST:     ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGNCA
genomic: ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
EST: gi|32931812|gb|CF036624.1|CF036624
EST:     ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTTGGACCATGGTATTCG
genomic: ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTTGGACCATGGTATTCG
EST: gi|60348576|gb|DN215549.1|DN215549
EST:     ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
genomic: ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
EST: gi|19058809|gb|BM737476.1|BM737476
EST:     ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
genomic: ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
EST: gi|21432105|gb|BQ547595.1|BQ547595
EST:     ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
genomic: ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
EST: gi|21432359|gb|BQ547849.1|BQ547849
EST:     ATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
genomic: ATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
EST: gi|86468581|gb|DY234951.1|DY234951
EST:     ACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
genomic: ACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCA
EST: gi|32930836|gb|CF035648.1|CF035648
EST:     ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACG                         ATTCATTGAAGTT
genomic: ATTTGAAGATAATGACATTTCAAGCAAATCCCTTCTAAGTTGTATTGACGgtactatttt ... tctttgctagATTCATTGAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgcattttctgctgtctaaaaactcatgcaaattgctggtttctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCATGACATCCAGAGCACAACTTCATGACTTGGAACATGGTCACTATGAGAT
                 gtctaaa  putative branch site (score: 3)
                                           tttctttgct  putative PPT
                  tctaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattttcgtacagtgtaccatcctttttttttccagtgcatatgcattttctgctgtctaaaaactcatgcaaattgctggtttctttgctagATTCATTGAAGTTGGACCATGGTATTCGCGAGAATGTGAAATCCATCGTCATGACATCCAGAGCACAACTTCATGACTTGGAACATGGTCACTATGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA