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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctctctgccagttccctcgtgtttcaaaacagagctcgagttcaaattgcttatttagtttcttttttctcttcttacttattgacaacttgttcacagGGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTCTACTG

Basic information

species Zea mays
transcript GRMZM2G157034_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|148969156|gb|EE019897.2|EE019897
EST:     CACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAG                         GGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
genomic: CACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAGgtgagctacg ... ttgttcacagGGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
EST: gi|149042078|gb|EE047056.2|EE047056
EST:     CACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAG                         GGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
genomic: CACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAGgtgagctacg ... ttgttcacagGGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
EST: gi|148960783|gb|EE011443.2|EE011443
EST:     GCCGCCACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAG                         GGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
genomic: GCCGCCACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAGgtgagctacg ... ttgttcacagGGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
EST: gi|148939524|gb|EC884116.2|EC884116
EST:     CACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAG                         GGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
genomic: CACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAGgtgagctacg ... ttgttcacagGGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
EST: gi|37417485|gb|CF646397.1|CF646397
EST:     ACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAG                         GGGTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC
genomic: ACATCCGTCCGGGCATCCTCGTCTCCCCAGCCCCGCTGCCGCAGgtgagctacg ... ttgttcacagGGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgcttatttagtttcttttttctcttcttacttattgacaacttgttcacagGGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTCTACTG
                                   tattgac  putative branch site (score: 2)
                                            cttgttc  putative PPT
      ttatttagtttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctctctgccagttccctcgtgtttcaaaacagagctcgagttcaaattgcttatttagtttcttttttctcttcttacttattgacaacttgttcacagGGTTCATCAGCAGAAGCTGCTTGCACCGCCGCCGCCGCCCTCTTCCTGTTCTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT