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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttttgcacaagaatatttaaattcaaacaagttatctttatttgatgtactgtaacaaccagagcttatcatgattgcatcttttgctacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCGAGGGGTTTGACAGAGGCGGCAAAACTGACAAATGCGGACCAGAAGTATA

Basic information

species Zea mays
transcript GRMZM5G896731_T03
intron # 8
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|32933882|gb|CF038694.1|CF038694
EST:     GTCCTAAAGCCTTTGTTCTTCAGAAGTTCAGTAGGACTGGTCGTGAACGG                         ATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
genomic: ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGGgtaaacatgt ... tacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
EST: gi|60358732|gb|DN225705.1|DN225705
EST:     ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG                         ATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
genomic: ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGGgtaaacatgt ... tacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
EST: gi|78085319|gb|DV513712.1|DV513712
EST:     ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG                         ATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
genomic: ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGGgtaaacatgt ... tacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
EST: gi|89250808|gb|DY622594.1|DY622594
EST:     ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGCCGTGAACGG                         ATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
genomic: ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGGgtaaacatgt ... tacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
EST: gi|86468848|gb|DY235218.1|DY235218
EST:     ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG                         ATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
genomic: ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGGgtaaacatgt ... tacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
EST: gi|78109135|gb|DV527552.1|DV527552
EST:     ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG                         ATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG
genomic: ATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGGgtaaacatgt ... tacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgtactgtaacaaccagagcttatcatgattgcatcttttgctacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCGAGGGGTTTGACAGAGGCGGCAAAACTGACAAATGCGGACCAGAAGTATA
       ctgtaac  putative branch site (score: 3)
                                     tcttttgct  putative PPT
                       ttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttttgcacaagaatatttaaattcaaacaagttatctttatttgatgtactgtaacaaccagagcttatcatgattgcatcttttgctacaacctagATCGATTCAGCCGTGAGAGAGGGTGTCGATATTCTGAAGATGGTGGCTGCGAGGGGTTTGACAGAGGCGGCAAAACTGACAAATGCGGACCAGAAGTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT