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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttcattctaacctgtatagttttttgaacactttgtagtgtagttatgcagccatgtgcaattggaatagccatgtcaagcctaatttcaggcttcagtaaagctagaatgctcttcttttggggggtaaactaacttcaatgctaatttactaatcaacatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGCAGATGCAAATGAAGTTGTTGAAAATTCA

Basic information

species Zea mays
transcript GRMZM2G106056_T03
intron # 20
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|60354502|gb|DN221475.1|DN221475
EST:     AGAGGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAG                         GTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
genomic: AGAGGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAGgttgttcatt ... acatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
EST: gi|87156002|gb|DY400791.1|DY400791
EST:     CAGACCACTCTTAGTTTCAGCCAGTCAAG                         GTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
genomic: CAGACCACTCTTAGTTTCAGCCAGTCAAGgttgttcatt ... acatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
EST: gi|211389765|gb|FL034465.1|FL034465
EST:     GGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAG                         GTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
genomic: GGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAGgttgttcatt ... acatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
EST: gi|60345446|gb|DN212419.1|DN212419
EST:     AGAGGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAG                         GTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
genomic: AGAGGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAGgttgttcatt ... acatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
EST: gi|91052428|gb|EB162846.1|EB162846
EST:     AGAGGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAG                         GTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
genomic: AGAGGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAGgttgttcatt ... acatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
EST: gi|211359817|gb|FL457852.1|FL457852
EST:     AGAGGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAG                         GTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC
genomic: AGAGGCACCAGTTCAATGAAGCAGACCACTCTTAGTTTCAGCCAGTCAAGgttgttcatt ... acatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttttggggggtaaactaacttcaatgctaatttactaatcaacatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGCAGATGCAAATGAAGTTGTTGAAAATTCA
                                    tactaat  putative branch site (score: 1)
                               taatttactaatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttcattctaacctgtatagttttttgaacactttgtagtgtagttatgcagccatgtgcaattggaatagccatgtcaagcctaatttcaggcttcagtaaagctagaatgctcttcttttggggggtaaactaacttcaatgctaatttactaatcaacatttgcagGTCAGCTACCGTTATTCGTAGTGAGGATGTGGCTTCCTCTGAGGAGGAAGCAGATGCAAATGAAGTTGTTGAAAATTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG