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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattaacggaatacctgttgcaaaactccatttgaatcagaaacgtatcttatatggtttgtcttctaaggaaccacctttgttttccctcctaattcttgcagAATTTCTTCTTTGAAATCATCAATGGTCTACGGCCAGCAAACACTGCAGGTTGCAGTTCATCAACCGATGCACCTAACATCCCACATG

Basic information

species Zea mays
transcript GRMZM2G081642_T01
intron # 9
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|166588412|gb|EG117001.1|EG117001
EST:     GATCAAAGCTTCATATGGGAGCATTTAAAGTTGGTAACATAACCAATGAG                         AATTTCTTCTTTGAAATCATCAATGGTC
genomic: GATCAAAGCTTCATATGGGAGCATTTAAAGTTGGTAACATAACCAATGAGgtaaattaac ... attcttgcagAATTTCTTCTTTGAAATCATCAATGGTC
EST: gi|21481154|gb|BQ577837.1|BQ577837
EST:     GATCAAAGCTTCATATGGGAGCATTTAAAGTTGGTAACATAACCAATGAG                         AATTTCTTCTTTGAAATCATCAATGGTCTACGGCCAGCAAACACTGCAGGT
genomic: GATCAAAGCTTCATATGGGAGCATTTAAAGTTGGTAACATAACCAATGAGgtaaattaac ... attcttgcagAATTTCTTCTTTGAAATCATCAATGGTCTACGGCCAGCAAACACTGCAGGT
EST: gi|21329781|gb|BQ485162.1|BQ485162
EST:     GATCAAAGCTTCATATGGGAGCATTTAAAGTTGGTAACATAACCAATGAG                         AATTTCTTCTTTGAAATCATCAATGGTCTACGGCCAGCAAACACTGCAGGT
genomic: GATCAAAGCTTCATATGGGAGCATTTAAAGTTGGTAACATAACCAATGAGgtaaattaac ... attcttgcagAATTTCTTCTTTGAAATCATCAATGGTCTACGGCCAGCAAACACTGCAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatggtttgtcttctaaggaaccacctttgttttccctcctaattcttgcagAATTTCTTCTTTGAAATCATCAATGGTCTACGGCCAGCAAACACTGCAGGTTGCAGTTCATCAACCGATGCACCTAACATCCCACATG
                                        tcctaat  putative branch site (score: 2)
                        ccacctttgttttccc  CT-rich tract
                             tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattaacggaatacctgttgcaaaactccatttgaatcagaaacgtatcttatatggtttgtcttctaaggaaccacctttgttttccctcctaattcttgcagAATTTCTTCTTTGAAATCATCAATGGTCTACGGCCAGCAAACACTGCAGGTTGCAGTTCATCAACCGATGCACCTAACATCCCACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG