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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatagtatgcccaggggggaaaatctgtgtaagcatgtatgcaattgacatattacttctttgtgtcctgattcgcttttgttgctccaattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGCAAGTGATTTCATTATGAAAGACTGGTCTATTTTCTCCAAACTTGATCAC

Basic information

species Zea mays
transcript GRMZM2G095778_T01
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|76909884|gb|DV163586.1|DV163586
EST:     ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAG                         ATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
genomic: ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAGgttcggcgct ... caattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
EST: gi|76015882|gb|DT943052.1|DT943052
EST:     ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAG                         ATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
genomic: ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAGgttcggcgct ... caattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
EST: gi|149086274|gb|EE175815.2|EE175815
EST:     ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAG                         ATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
genomic: ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAGgttcggcgct ... caattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
EST: gi|71426823|gb|DR807873.1|DR807873
EST:     ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAG                         ATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
genomic: ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAGgttcggcgct ... caattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
EST: gi|78116957|gb|DV535344.1|DV535344
EST:     ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAG                         ATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
genomic: ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAGgttcggcgct ... caattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
EST: gi|211542643|gb|FL069010.1|FL069010
EST:     ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAG                         ATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
genomic: ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAGgttcggcgct ... caattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
EST: gi|149106846|gb|EE188744.2|EE188744
EST:     ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAG                         ATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
genomic: ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAGgttcggcgct ... caattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
EST: gi|89760692|gb|DY689001.1|DY689001
EST:     ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAG                         ATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC
genomic: ACGACGGTCACCATCAGCCACCGCGCGATCCCGGGGGACGGCCAGGCCAGgttcggcgct ... caattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgacatattacttctttgtgtcctgattcgcttttgttgctccaattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGCAAGTGATTTCATTATGAAAGACTGGTCTATTTTCTCCAAACTTGATCAC
                       tcctgat  putative branch site (score: 3)
                                       ttgctcc  putative PPT
       atattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatagtatgcccaggggggaaaatctgtgtaagcatgtatgcaattgacatattacttctttgtgtcctgattcgcttttgttgctccaattggcagATTCCACAACGTTTTACTCTTATTAAACTCCCCAACTTCGTCTAAGGAAGCAAGTGATTTCATTATGAAAGACTGGTCTATTTTCTCCAAACTTGATCAC

- - - -gtatgcc
- - - - - - - - - - - - - - - - - - - tgtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct